[2024-01-24 15:26:36,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:36,749] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:36,749] [INFO] DQC Reference Directory: /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference
[2024-01-24 15:26:39,059] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:39,061] [INFO] Task started: Prodigal
[2024-01-24 15:26:39,062] [INFO] Running command: gunzip -c /var/lib/cwl/stga76cecd3-0770-4664-bc30-cc0cca92e3a0/GCF_900078665.2_PRJEB13221_genomic.fna.gz | prodigal -d GCF_900078665.2_PRJEB13221_genomic.fna/cds.fna -a GCF_900078665.2_PRJEB13221_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:08,230] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:08,231] [INFO] Task started: HMMsearch
[2024-01-24 15:27:08,231] [INFO] Running command: hmmsearch --tblout GCF_900078665.2_PRJEB13221_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/reference_markers.hmm GCF_900078665.2_PRJEB13221_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:08,562] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:08,563] [INFO] Found 6/6 markers.
[2024-01-24 15:27:08,618] [INFO] Query marker FASTA was written to GCF_900078665.2_PRJEB13221_genomic.fna/markers.fasta
[2024-01-24 15:27:08,619] [INFO] Task started: Blastn
[2024-01-24 15:27:08,619] [INFO] Running command: blastn -query GCF_900078665.2_PRJEB13221_genomic.fna/markers.fasta -db /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/reference_markers.fasta -out GCF_900078665.2_PRJEB13221_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:10,021] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:10,025] [INFO] Selected 17 target genomes.
[2024-01-24 15:27:10,026] [INFO] Target genome list was writen to GCF_900078665.2_PRJEB13221_genomic.fna/target_genomes.txt
[2024-01-24 15:27:10,033] [INFO] Task started: fastANI
[2024-01-24 15:27:10,034] [INFO] Running command: fastANI --query /var/lib/cwl/stga76cecd3-0770-4664-bc30-cc0cca92e3a0/GCF_900078665.2_PRJEB13221_genomic.fna.gz --refList GCF_900078665.2_PRJEB13221_genomic.fna/target_genomes.txt --output GCF_900078665.2_PRJEB13221_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:36,126] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:36,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:36,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:36,143] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:36,144] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:36,144] [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 houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	99.9999	2135	2139	95	conclusive
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	86.7441	1707	2139	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	86.6352	1652	2139	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	86.557	1618	2139	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	86.5427	1638	2139	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	86.1546	1578	2139	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	86.0154	1639	2139	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	86.01	1634	2139	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	86.0056	1646	2139	95	below_threshold
Mycolicibacterium setense	strain=DSM 45070	GCA_000805385.1	431269	431269	type	True	85.8809	1619	2139	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	85.5377	1396	2139	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	85.4892	1467	2139	95	below_threshold
[Mycobacterium] fortunisiensis	strain=TNTM28	GCA_019050325.1	2600579	2600579	type	True	85.3701	1392	2139	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.3087	938	2139	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.8645	879	2139	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.742	864	2139	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.7131	895	2139	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:36,146] [INFO] DFAST Taxonomy check result was written to GCF_900078665.2_PRJEB13221_genomic.fna/tc_result.tsv
[2024-01-24 15:27:36,146] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:36,147] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:36,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/checkm_data
[2024-01-24 15:27:36,149] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:36,207] [INFO] Task started: CheckM
[2024-01-24 15:27:36,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900078665.2_PRJEB13221_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900078665.2_PRJEB13221_genomic.fna/checkm_input GCF_900078665.2_PRJEB13221_genomic.fna/checkm_result
[2024-01-24 15:28:58,714] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:58,717] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:58,741] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:58,741] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:58,742] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900078665.2_PRJEB13221_genomic.fna/markers.fasta)
[2024-01-24 15:28:58,743] [INFO] Task started: Blastn
[2024-01-24 15:28:58,743] [INFO] Running command: blastn -query GCF_900078665.2_PRJEB13221_genomic.fna/markers.fasta -db /var/lib/cwl/stg44df2ff6-43b7-4e45-9b6b-27d93694a5ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_900078665.2_PRJEB13221_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:00,830] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:00,835] [INFO] Selected 16 target genomes.
[2024-01-24 15:29:00,835] [INFO] Target genome list was writen to GCF_900078665.2_PRJEB13221_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:00,849] [INFO] Task started: fastANI
[2024-01-24 15:29:00,849] [INFO] Running command: fastANI --query /var/lib/cwl/stga76cecd3-0770-4664-bc30-cc0cca92e3a0/GCF_900078665.2_PRJEB13221_genomic.fna.gz --refList GCF_900078665.2_PRJEB13221_genomic.fna/target_genomes_gtdb.txt --output GCF_900078665.2_PRJEB13221_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:29:26,248] [INFO] Task succeeded: fastANI
[2024-01-24 15:29:26,268] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:29:26,269] [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_900078665.2	s__Mycobacterium houstonense	99.9999	2135	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001245615.1	s__Mycobacterium neworleansense	86.7418	1707	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731295.1	s__Mycobacterium boenickei	86.6324	1653	2139	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	86.5257	1641	2139	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	86.5207	1579	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086835.1	s__Mycobacterium porcinum	86.2768	1628	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_004762045.1	s__Mycobacterium sp004762045	86.2012	1613	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009729095.1	s__Mycobacterium sp009729095	86.1238	1498	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_000723385.1	s__Mycobacterium farcinogenes	86.0785	1586	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_000295855.1	s__Mycobacterium fortuitum	86.0046	1641	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	85.7436	1633	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000426065.1	s__Mycobacterium sp000426065	85.5618	1634	2139	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	85.5486	1562	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_017876775.1	s__Mycobacterium lutetiense	85.4885	1467	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	85.3746	1390	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954135.1	s__Mycobacterium sp001954135	85.082	1418	2139	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:29:26,270] [INFO] GTDB search result was written to GCF_900078665.2_PRJEB13221_genomic.fna/result_gtdb.tsv
[2024-01-24 15:29:26,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:29:26,274] [INFO] DFAST_QC result json was written to GCF_900078665.2_PRJEB13221_genomic.fna/dqc_result.json
[2024-01-24 15:29:26,275] [INFO] DFAST_QC completed!
[2024-01-24 15:29:26,275] [INFO] Total running time: 0h2m50s