15:35:15 | INFO | Making a new reference for: /bank/experiments/2023-09-jordi/Smed/Smed.fa.
15:35:15 | INFO | You say the gimme.vertebrate.v5.0 database is based on: GRCh38.p13 & GRCm38.p6.
15:35:15 | INFO | For better orthology inference we are also using these assemblies: GRCz11 & GRCg6a & UCB_Xtro_10.0 & BraLan3 & ASM223467v1 & ARS-UCD1.2 & phaCin_unsw_v4.1 & rCheMyd1.pri.v2 & Mlig_3_7 & El_Paco_v._4 & BDGP6.46 & Hydra_105_v3 & WBcel235 & KH & ASM20922v1.
15:35:15 | INFO | Using lenient strategy for orthology/name inference.
15:35:15 | INFO | genomes_dir: /bank/experiments/2023-09-jordi/genomes
15:35:15 | INFO | tmpdir: /bank/experiments/2023-09-jordi/latest/orthofinder_output
15:35:15 | INFO | outdir: /bank/experiments/2023-09-jordi/latest
15:35:15 | INFO | Downloading all assemblies.
15:35:15 | INFO | ASM223467v1 was already downloaded, using that version.
15:35:15 | INFO | GRCg6a was already downloaded, using that version.
15:35:15 | INFO | BraLan3 was already downloaded, using that version.
15:35:15 | INFO | Smed was already downloaded, using that version.
15:35:15 | INFO | ASM20922v1 was already downloaded, using that version.
15:35:15 | INFO | Hydra_105_v3 was already downloaded, using that version.
15:35:15 | INFO | ARS-UCD1.2 was already downloaded, using that version.
15:35:15 | INFO | rCheMyd1.pri.v2 was already downloaded, using that version.
15:35:15 | INFO | GRCz11 was already downloaded, using that version.
15:35:15 | INFO | El_Paco_v._4 was already downloaded, using that version.
15:35:15 | INFO | UCB_Xtro_10.0 was already downloaded, using that version.
15:35:15 | INFO | Mlig_3_7 was already downloaded, using that version.
15:35:15 | INFO | phaCin_unsw_v4.1 was already downloaded, using that version.
15:35:15 | INFO | BDGP6.46 was already downloaded, using that version.
15:35:15 | INFO | KH was already downloaded, using that version.
15:35:15 | INFO | WBcel235 was already downloaded, using that version.
15:35:28 | INFO | Downloading GRCm38.p6 through genomepy.
15:35:43 | WARNING | GENCODE appears to be offline.
15:35:48 | INFO | Downloading genome from NCBI. Target URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.fna.gz...

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15:36:20 | INFO | Genome download successful, starting post processing...

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15:36:47 | INFO | name: GRCm38.p6
15:36:47 | INFO | local name: GRCm38.p6
15:36:47 | INFO | fasta: /bank/experiments/2023-09-jordi/genomes/GRCm38.p6/GRCm38.p6.fa

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15:37:47 | INFO | Downloading annotation from NCBI. Target URL: https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/635/GCF_000001635.26_GRCm38.p6/GCF_000001635.26_GRCm38.p6_genomic.gff.gz...

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15:38:05 | INFO | Annotation download successful
15:38:30 | INFO | Downloading GRCh38.p13 through genomepy.
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15:39:10 | INFO | Genome download successful, starting post processing...

Processing NCBI Fasta: 0.00 lines [00:00, ? lines/s]
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15:39:42 | INFO | name: GRCh38.p13
15:39:42 | INFO | local name: GRCh38.p13
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15:41:14 | INFO | Annotation download successful
15:41:55 | INFO | Taking the longest protein per gene per assembly.
15:41:55 | INFO | Processing ASM223467v1.
15:42:04 | INFO | Processing GRCg6a.
15:42:18 | INFO | Processing GRCm38.p6.
15:42:38 | INFO | Processing BraLan3.
15:42:45 | INFO | Processing Smed.
15:42:54 | INFO | Processing ASM20922v1.
15:42:59 | INFO | Processing GRCh38.p13.
15:43:22 | INFO | Processing Hydra_105_v3.
15:43:31 | INFO | Processing ARS-UCD1.2.
15:43:49 | INFO | Processing rCheMyd1.pri.v2.
15:44:06 | INFO | Processing GRCz11.
15:44:18 | INFO | Processing El_Paco_v._4.
15:44:22 | INFO | Processing UCB_Xtro_10.0.
15:44:37 | INFO | Processing Mlig_3_7.
15:44:45 | INFO | Processing phaCin_unsw_v4.1.
15:45:05 | INFO | Processing BDGP6.46.
15:45:09 | INFO | Processing KH.
15:45:13 | INFO | Processing WBcel235.
15:45:16 | INFO | Running orthofinder to find orthologs.
16:24:25 | INFO | Storing everything in a database.
/home/siebrenf/miniconda3/envs/jordi/lib/python3.10/site-packages/pandas/util/_decorators.py:211: DtypeWarning: Columns (3,4,5,6,7,8,9,10,11,12,13,14,15) have mixed types. Specify dtype option on import or set low_memory=False.
  return func(*args, **kwargs)
/home/siebrenf/miniconda3/envs/jordi/lib/python3.10/site-packages/pandas/util/_decorators.py:211: DtypeWarning: Columns (1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,17,18) have mixed types. Specify dtype option on import or set low_memory=False.
  return func(*args, **kwargs)
16:24:33 | INFO | Now writing your motif2factors files.
16:24:34 | INFO | No orthologs found for TF ENSG00000234254.
16:24:39 | INFO | No orthologs found for TF ENSMUSG00000044690.
16:24:39 | INFO | No orthologs found for TF ENSG00000235187.
16:24:42 | INFO | No orthologs found for TF AC012531.1.
16:24:46 | INFO | No orthologs found for TF EBOX.
16:24:49 | INFO | No orthologs found for TF Gm4830.
16:24:50 | INFO | No orthologs found for TF Q8VHG7_MOUSE.
16:24:50 | INFO | No orthologs found for TF ENSMUSG00000040953.
16:24:51 | INFO | No orthologs found for TF Gm5889.
16:24:53 | INFO | No orthologs found for TF ENSG00000187728.
16:24:58 | INFO | No orthologs found for TF CR933878.8.
16:24:59 | INFO | No orthologs found for TF BX927239.6.
16:25:00 | INFO | No orthologs found for TF AL845464.3.
16:25:01 | INFO | No orthologs found for TF CR812478.2.
16:25:01 | INFO | No orthologs found for TF BX284686.1.
16:25:02 | INFO | No orthologs found for TF AL662830.5.
16:25:05 | INFO | No orthologs found for TF ENSG00000250096.
16:25:06 | INFO | No orthologs found for TF CR388229.2.
16:25:07 | INFO | No orthologs found for TF AL662833.4.
16:25:08 | INFO | No orthologs found for TF BX088580.2.
16:25:09 | INFO | No orthologs found for TF AL773544.1.
16:25:09 | INFO | No orthologs found for TF CR759815.4.
16:25:11 | INFO | No orthologs found for TF IRC900814.
16:25:13 | INFO | No orthologs found for TF CR936877.3.
16:25:14 | INFO | No orthologs found for TF CR354565.3.
16:25:15 | INFO | No orthologs found for TF AL844527.7.
16:25:15 | INFO | No orthologs found for TF AL662824.5.
16:25:16 | INFO | No orthologs found for TF CR759733.4.
16:25:18 | INFO | No orthologs found for TF ENSMUSG00000090020.
16:25:21 | INFO | No orthologs found for TF CACBP.
16:25:22 | INFO | No orthologs found for TF AC002126.6.
16:25:25 | INFO | No orthologs found for TF ENSMUSG00000079994.
16:25:34 | INFO | No orthologs found for TF mix-a.
16:25:35 | INFO | No orthologs found for TF ENSG00000250811.
16:25:36 | INFO | No orthologs found for TF Rbpsuh-rs3.
16:25:49 | INFO | No orthologs found for TF AC189028.1.
16:25:51 | INFO | No orthologs found for TF NPAS.
16:26:11 | INFO | No orthologs found for TF Gm5454.
16:26:16 | INFO | No orthologs found for TF HINFP1.
16:26:22 | INFO | No orthologs found for TF Zscan4-ps2.
16:26:23 | INFO | No orthologs found for TF AL662834.13.
16:26:24 | INFO | No orthologs found for TF CR759784.3.
16:26:25 | INFO | No orthologs found for TF CR388219.4.
16:26:26 | INFO | No orthologs found for TF AL844853.8.
16:26:27 | INFO | No orthologs found for TF ENSG00000224558.
16:26:28 | INFO | No orthologs found for TF ENSG00000234550.
16:26:29 | INFO | No orthologs found for TF ENSG00000237516.
16:26:29 | INFO | No orthologs found for TF ENSG00000233361.
16:26:30 | INFO | No orthologs found for TF DUX4L5.
16:26:31 | INFO | No orthologs found for TF ENSG00000226866.
16:26:32 | INFO | No orthologs found for TF ENSG00000230776.
16:26:33 | INFO | No orthologs found for TF CT476828.2.
16:26:34 | INFO | No orthologs found for TF ENSG00000228710.
16:26:35 | INFO | No orthologs found for TF ENSG00000236207.
16:26:35 | INFO | No orthologs found for TF ENSG00000250589.
16:26:36 | INFO | No orthologs found for TF DUX4L3.
16:26:37 | INFO | No orthologs found for TF DUX4L6.
16:26:38 | INFO | No orthologs found for TF AL592170.2.
16:26:39 | INFO | No orthologs found for TF ENSG00000233294.
16:26:40 | INFO | No orthologs found for TF ENSG00000227522.
16:26:41 | INFO | No orthologs found for TF ENSG00000215754.
16:26:42 | INFO | No orthologs found for TF ENSG00000232923.
16:26:42 | INFO | No orthologs found for TF DUX4L2.
16:26:43 | INFO | No orthologs found for TF ENSG00000217642.
16:26:44 | INFO | No orthologs found for TF ENSG00000233698.
16:26:45 | INFO | No orthologs found for TF ENSG00000230380.
16:26:46 | INFO | No orthologs found for TF ENSG00000225958.
16:26:47 | INFO | No orthologs found for TF ENSG00000233794.
16:26:48 | INFO | No orthologs found for TF NR1H.
16:26:49 | INFO | No orthologs found for TF EWSR1-FLI1.
16:26:52 | INFO | No orthologs found for TF Srebp1a.
16:26:53 | INFO | No orthologs found for TF AC168977.1.
16:26:59 | INFO | No orthologs found for TF CR753803.1.
16:27:00 | INFO | No orthologs found for TF AL662828.6.
16:27:01 | INFO | No orthologs found for TF CR925796.2.
16:27:03 | INFO | No orthologs found for TF AC226150.2.
16:27:06 | INFO | No orthologs found for TF GTF2A.
16:27:07 | INFO | No orthologs found for TF COMP1.
16:27:09 | INFO | No orthologs found for TF HF1H3B.
16:27:12 | INFO | No orthologs found for TF ENSG00000250542.
16:27:15 | INFO | No orthologs found for TF GRE.