[2024-01-25 17:34:07,121] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:34:07,125] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:34:07,125] [INFO] DQC Reference Directory: /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference
[2024-01-25 17:34:09,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:34:09,028] [INFO] Task started: Prodigal
[2024-01-25 17:34:09,029] [INFO] Running command: gunzip -c /var/lib/cwl/stge8778eb5-6422-4ccc-9b91-cab61a2cf96f/GCF_000295855.1_ASM29585v1_genomic.fna.gz | prodigal -d GCF_000295855.1_ASM29585v1_genomic.fna/cds.fna -a GCF_000295855.1_ASM29585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:34:29,495] [INFO] Task succeeded: Prodigal
[2024-01-25 17:34:29,496] [INFO] Task started: HMMsearch
[2024-01-25 17:34:29,496] [INFO] Running command: hmmsearch --tblout GCF_000295855.1_ASM29585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/reference_markers.hmm GCF_000295855.1_ASM29585v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:34:29,856] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:34:29,857] [INFO] Found 6/6 markers.
[2024-01-25 17:34:29,909] [INFO] Query marker FASTA was written to GCF_000295855.1_ASM29585v1_genomic.fna/markers.fasta
[2024-01-25 17:34:29,909] [INFO] Task started: Blastn
[2024-01-25 17:34:29,909] [INFO] Running command: blastn -query GCF_000295855.1_ASM29585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/reference_markers.fasta -out GCF_000295855.1_ASM29585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:34:31,045] [INFO] Task succeeded: Blastn
[2024-01-25 17:34:31,049] [INFO] Selected 15 target genomes.
[2024-01-25 17:34:31,049] [INFO] Target genome list was writen to GCF_000295855.1_ASM29585v1_genomic.fna/target_genomes.txt
[2024-01-25 17:34:31,078] [INFO] Task started: fastANI
[2024-01-25 17:34:31,078] [INFO] Running command: fastANI --query /var/lib/cwl/stge8778eb5-6422-4ccc-9b91-cab61a2cf96f/GCF_000295855.1_ASM29585v1_genomic.fna.gz --refList GCF_000295855.1_ASM29585v1_genomic.fna/target_genomes.txt --output GCF_000295855.1_ASM29585v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:34:54,497] [INFO] Task succeeded: fastANI
[2024-01-25 17:34:54,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:34:54,498] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:34:54,508] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 17:34:54,508] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:34:54,508] [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 fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	100.0	2065	2075	95	conclusive
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	99.9637	2051	2075	95	conclusive
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	98.7053	1926	2075	95	conclusive
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	88.0962	1714	2075	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	87.0506	1637	2075	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	87.0201	1648	2075	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	87.0071	1659	2075	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	86.9989	1671	2075	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	86.8875	1690	2075	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	86.3131	1459	2075	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	85.9027	1629	2075	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4433	841	2075	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.3707	823	2075	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.3604	863	2075	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.0462	862	2075	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:34:54,510] [INFO] DFAST Taxonomy check result was written to GCF_000295855.1_ASM29585v1_genomic.fna/tc_result.tsv
[2024-01-25 17:34:54,510] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:34:54,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:34:54,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/checkm_data
[2024-01-25 17:34:54,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:34:54,568] [INFO] Task started: CheckM
[2024-01-25 17:34:54,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000295855.1_ASM29585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000295855.1_ASM29585v1_genomic.fna/checkm_input GCF_000295855.1_ASM29585v1_genomic.fna/checkm_result
[2024-01-25 17:35:55,440] [INFO] Task succeeded: CheckM
[2024-01-25 17:35:55,441] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:35:55,495] [INFO] ===== Completeness check finished =====
[2024-01-25 17:35:55,495] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:35:55,496] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000295855.1_ASM29585v1_genomic.fna/markers.fasta)
[2024-01-25 17:35:55,497] [INFO] Task started: Blastn
[2024-01-25 17:35:55,497] [INFO] Running command: blastn -query GCF_000295855.1_ASM29585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge84560ed-1390-40b7-b659-38c8a9cb26ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_000295855.1_ASM29585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:35:57,301] [INFO] Task succeeded: Blastn
[2024-01-25 17:35:57,303] [INFO] Selected 15 target genomes.
[2024-01-25 17:35:57,304] [INFO] Target genome list was writen to GCF_000295855.1_ASM29585v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:35:57,311] [INFO] Task started: fastANI
[2024-01-25 17:35:57,312] [INFO] Running command: fastANI --query /var/lib/cwl/stge8778eb5-6422-4ccc-9b91-cab61a2cf96f/GCF_000295855.1_ASM29585v1_genomic.fna.gz --refList GCF_000295855.1_ASM29585v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000295855.1_ASM29585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:36:21,579] [INFO] Task succeeded: fastANI
[2024-01-25 17:36:21,591] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:36:21,592] [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_000295855.1	s__Mycobacterium fortuitum	100.0	2065	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	conclusive
GCF_001665625.1	s__Mycobacterium peregrinum_B	88.1225	1701	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.32	98.32	0.89	0.89	2	-
GCF_002102345.1	s__Mycobacterium peregrinum	88.0976	1715	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	87.9551	1706	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000723385.1	s__Mycobacterium farcinogenes	87.2159	1649	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_002086835.1	s__Mycobacterium porcinum	87.1413	1652	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_010731295.1	s__Mycobacterium boenickei	87.0146	1668	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_000455325.1	s__Mycobacterium septicum	87.0112	1658	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_001942045.1	s__Mycobacterium porcinum_A	86.9671	1609	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004762045.1	s__Mycobacterium sp004762045	86.6911	1647	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010727325.1	s__Mycobacterium alvei	86.3012	1461	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	86.036	1601	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_900078665.2	s__Mycobacterium houstonense	85.914	1627	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953975.1	s__Mycobacterium sp001953975	84.9943	1426	2075	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	98.19	0.92	0.92	2	-
GCF_001665685.1	s__Mycobacterium sp001665685	81.5164	1191	2075	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 17:36:21,593] [INFO] GTDB search result was written to GCF_000295855.1_ASM29585v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:36:21,594] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:36:21,597] [INFO] DFAST_QC result json was written to GCF_000295855.1_ASM29585v1_genomic.fna/dqc_result.json
[2024-01-25 17:36:21,598] [INFO] DFAST_QC completed!
[2024-01-25 17:36:21,598] [INFO] Total running time: 0h2m14s