[2024-01-25 17:54:35,690] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:54:35,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:54:35,692] [INFO] DQC Reference Directory: /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference
[2024-01-25 17:54:36,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:54:36,826] [INFO] Task started: Prodigal
[2024-01-25 17:54:36,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg26f26c72-ffa4-468c-8c6f-08567ce5a613/GCF_025821625.1_ASM2582162v1_genomic.fna.gz | prodigal -d GCF_025821625.1_ASM2582162v1_genomic.fna/cds.fna -a GCF_025821625.1_ASM2582162v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:54:54,907] [INFO] Task succeeded: Prodigal
[2024-01-25 17:54:54,908] [INFO] Task started: HMMsearch
[2024-01-25 17:54:54,908] [INFO] Running command: hmmsearch --tblout GCF_025821625.1_ASM2582162v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/reference_markers.hmm GCF_025821625.1_ASM2582162v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:54:55,192] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:54:55,193] [INFO] Found 6/6 markers.
[2024-01-25 17:54:55,249] [INFO] Query marker FASTA was written to GCF_025821625.1_ASM2582162v1_genomic.fna/markers.fasta
[2024-01-25 17:54:55,249] [INFO] Task started: Blastn
[2024-01-25 17:54:55,249] [INFO] Running command: blastn -query GCF_025821625.1_ASM2582162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/reference_markers.fasta -out GCF_025821625.1_ASM2582162v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:54:56,388] [INFO] Task succeeded: Blastn
[2024-01-25 17:54:56,392] [INFO] Selected 26 target genomes.
[2024-01-25 17:54:56,393] [INFO] Target genome list was writen to GCF_025821625.1_ASM2582162v1_genomic.fna/target_genomes.txt
[2024-01-25 17:54:56,416] [INFO] Task started: fastANI
[2024-01-25 17:54:56,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f26c72-ffa4-468c-8c6f-08567ce5a613/GCF_025821625.1_ASM2582162v1_genomic.fna.gz --refList GCF_025821625.1_ASM2582162v1_genomic.fna/target_genomes.txt --output GCF_025821625.1_ASM2582162v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:27,951] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:27,951] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:27,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:27,966] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:27,967] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:27,967] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Mycolicibacterium chlorophenolicum	strain=DSM 43826	GCA_001044235.1	37916	37916	type	True	83.8123	1311	2114	95	below_threshold
Mycolicibacterium chlorophenolicum	strain=NBRC 15527	GCA_001552315.1	37916	37916	type	True	83.7287	1309	2114	95	below_threshold
Mycolicibacterium vaccae	strain=NBRC 14118	GCA_001552715.1	1810	1810	type	True	82.4614	1126	2114	95	below_threshold
Mycolicibacterium vaccae	strain=95051	GCA_001655245.1	1810	1810	type	True	82.4219	1219	2114	95	below_threshold
Mycolicibacterium aurum	strain=NCTC10437	GCA_900637195.1	1791	1791	type	True	82.0478	1218	2114	95	below_threshold
Mycolicibacterium aurum	strain=NCTC 10437	GCA_001049355.1	1791	1791	type	True	81.9832	1213	2114	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	81.623	1115	2114	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	80.5951	971	2114	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	80.5576	984	2114	95	below_threshold
Mycolicibacterium elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	80.5261	975	2114	95	below_threshold
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	80.4587	972	2114	95	below_threshold
Mycolicibacterium arabiense	strain=JCM 18538	GCA_010731815.2	1286181	1286181	type	True	80.3671	973	2114	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	80.1928	1014	2114	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	80.1387	959	2114	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	80.123	918	2114	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	80.1206	933	2114	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	80.1186	984	2114	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.9937	669	2114	95	below_threshold
Mycolicibacterium thermoresistibile	strain=ATCC 19527	GCA_000234585.2	1797	1797	type	True	79.9722	843	2114	95	below_threshold
Mycolicibacterium thermoresistibile	strain=NCTC10409	GCA_900187065.1	1797	1797	type	True	79.9685	865	2114	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.8803	874	2114	95	below_threshold
Mycolicibacterium bacteremicum	strain=DSM 45578	GCA_002086115.1	564198	564198	type	True	79.834	952	2114	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7949	981	2114	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.7176	893	2114	95	below_threshold
Mycobacterium riyadhense	strain=DSM 45176	GCA_002101845.1	486698	486698	type	True	78.233	576	2114	95	below_threshold
Mycobacterium haemophilum	strain=ATCC 29548	GCA_000340435.3	29311	29311	type	True	78.0593	446	2114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:27,968] [INFO] DFAST Taxonomy check result was written to GCF_025821625.1_ASM2582162v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:27,969] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:27,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:27,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/checkm_data
[2024-01-25 17:55:27,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:28,032] [INFO] Task started: CheckM
[2024-01-25 17:55:28,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821625.1_ASM2582162v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821625.1_ASM2582162v1_genomic.fna/checkm_input GCF_025821625.1_ASM2582162v1_genomic.fna/checkm_result
[2024-01-25 17:56:27,379] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:27,380] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:27,401] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:27,402] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:27,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821625.1_ASM2582162v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:27,403] [INFO] Task started: Blastn
[2024-01-25 17:56:27,403] [INFO] Running command: blastn -query GCF_025821625.1_ASM2582162v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg803aaa04-73f6-4d8e-8d58-e819be763666/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821625.1_ASM2582162v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:29,087] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:29,090] [INFO] Selected 20 target genomes.
[2024-01-25 17:56:29,090] [INFO] Target genome list was writen to GCF_025821625.1_ASM2582162v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:29,105] [INFO] Task started: fastANI
[2024-01-25 17:56:29,105] [INFO] Running command: fastANI --query /var/lib/cwl/stg26f26c72-ffa4-468c-8c6f-08567ce5a613/GCF_025821625.1_ASM2582162v1_genomic.fna.gz --refList GCF_025821625.1_ASM2582162v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821625.1_ASM2582162v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:57,291] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:57,302] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:56:57,303] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_010723735.1	s__Mycobacterium hippocampi_B	84.7085	1402	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705885.1	s__Mycobacterium vanbaalenii_A	84.5173	1340	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005222675.1	s__Mycobacterium sp005222675	84.1964	1415	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013390125.1	s__Mycobacterium hippocampi_A	84.0154	1353	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	83.1314	1352	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_001545925.1	s__Mycobacterium sp001545925	82.7198	1035	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266905.1	s__Mycobacterium chubuense_A	82.6832	1243	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900454025.1	s__Mycobacterium gilvum	82.1742	1230	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.87	97.81	0.88	0.86	5	-
GCF_900637195.1	s__Mycobacterium aurum	82.0281	1221	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900108565.1	s__Mycobacterium rutilum	81.6338	1113	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	81.5769	1094	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500065.1	s__Mycobacterium sp001500065	80.5659	933	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240945.1	s__Mycobacterium sp900240945	80.3851	1013	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268465.1	s__Mycobacterium sp018268465	80.3173	912	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001499905.1	s__Mycobacterium sp001499905	80.2068	915	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667505.1	s__Mycobacterium sp001667505	80.0726	986	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826815.1	s__Mycobacterium sp902826815	79.8262	906	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402475.1	s__Mycobacterium sp003402475	79.2933	741	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455125.1	s__Mycobacterium sp000455125	78.6807	623	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.70	98.55	0.90	0.88	3	-
GCF_010723575.1	s__Mycobacterium bourgelatii	78.1937	658	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:57,304] [INFO] GTDB search result was written to GCF_025821625.1_ASM2582162v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:57,305] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:57,309] [INFO] DFAST_QC result json was written to GCF_025821625.1_ASM2582162v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:57,310] [INFO] DFAST_QC completed!
[2024-01-25 17:56:57,310] [INFO] Total running time: 0h2m22s