[2024-01-24 13:12:51,105] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:51,112] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:51,112] [INFO] DQC Reference Directory: /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference
[2024-01-24 13:12:52,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:52,421] [INFO] Task started: Prodigal
[2024-01-24 13:12:52,422] [INFO] Running command: gunzip -c /var/lib/cwl/stg7ecbe44b-53b6-4a39-b24a-daa0bcbfb3ff/GCF_017876775.1_ASM1787677v1_genomic.fna.gz | prodigal -d GCF_017876775.1_ASM1787677v1_genomic.fna/cds.fna -a GCF_017876775.1_ASM1787677v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:13,154] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:13,155] [INFO] Task started: HMMsearch
[2024-01-24 13:13:13,155] [INFO] Running command: hmmsearch --tblout GCF_017876775.1_ASM1787677v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/reference_markers.hmm GCF_017876775.1_ASM1787677v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:13,513] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:13,514] [INFO] Found 6/6 markers.
[2024-01-24 13:13:13,573] [INFO] Query marker FASTA was written to GCF_017876775.1_ASM1787677v1_genomic.fna/markers.fasta
[2024-01-24 13:13:13,573] [INFO] Task started: Blastn
[2024-01-24 13:13:13,573] [INFO] Running command: blastn -query GCF_017876775.1_ASM1787677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/reference_markers.fasta -out GCF_017876775.1_ASM1787677v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:14,874] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:14,878] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:14,879] [INFO] Target genome list was writen to GCF_017876775.1_ASM1787677v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:14,890] [INFO] Task started: fastANI
[2024-01-24 13:13:14,890] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ecbe44b-53b6-4a39-b24a-daa0bcbfb3ff/GCF_017876775.1_ASM1787677v1_genomic.fna.gz --refList GCF_017876775.1_ASM1787677v1_genomic.fna/target_genomes.txt --output GCF_017876775.1_ASM1787677v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:42,248] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:42,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:42,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:42,269] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:42,270] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:42,270] [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 lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	100.0	2110	2114	95	conclusive
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	91.8869	1609	2114	95	below_threshold
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	87.9164	1602	2114	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	87.7394	1617	2114	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	87.7245	1591	2114	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	87.5449	1564	2114	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	86.9637	1553	2114	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	86.8441	1554	2114	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	86.45	1527	2114	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	86.4329	1556	2114	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	85.4401	1472	2114	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	80.0745	852	2114	95	below_threshold
Candidatus Mycolicibacterium alkanivorans		GCA_022760805.1	2954114	2954114	type	True	79.8278	629	2114	95	below_threshold
Mycolicibacterium mengxianglii	strain=Z-34	GCA_015710575.2	2736649	2736649	type	True	79.5464	705	2114	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.5067	823	2114	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.4577	832	2114	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4486	827	2114	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.156	803	2114	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:42,272] [INFO] DFAST Taxonomy check result was written to GCF_017876775.1_ASM1787677v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:42,272] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:42,272] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:42,273] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/checkm_data
[2024-01-24 13:13:42,274] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:42,335] [INFO] Task started: CheckM
[2024-01-24 13:13:42,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017876775.1_ASM1787677v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017876775.1_ASM1787677v1_genomic.fna/checkm_input GCF_017876775.1_ASM1787677v1_genomic.fna/checkm_result
[2024-01-24 13:14:46,001] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:46,002] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:46,022] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:46,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:46,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017876775.1_ASM1787677v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:46,023] [INFO] Task started: Blastn
[2024-01-24 13:14:46,023] [INFO] Running command: blastn -query GCF_017876775.1_ASM1787677v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd99f2937-c207-4123-a90e-f3f69c9362d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_017876775.1_ASM1787677v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:47,837] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:47,840] [INFO] Selected 17 target genomes.
[2024-01-24 13:14:47,841] [INFO] Target genome list was writen to GCF_017876775.1_ASM1787677v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:47,853] [INFO] Task started: fastANI
[2024-01-24 13:14:47,854] [INFO] Running command: fastANI --query /var/lib/cwl/stg7ecbe44b-53b6-4a39-b24a-daa0bcbfb3ff/GCF_017876775.1_ASM1787677v1_genomic.fna.gz --refList GCF_017876775.1_ASM1787677v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017876775.1_ASM1787677v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:15,493] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:15,513] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:15,514] [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_017876775.1	s__Mycobacterium lutetiense	100.0	2110	2114	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_010727325.1	s__Mycobacterium alvei	91.8825	1610	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_011745145.1	s__Mycobacterium sp011745145	89.4211	1557	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_001665625.1	s__Mycobacterium peregrinum_B	88.1275	1543	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.32	98.32	0.89	0.89	2	-
GCF_001665785.1	s__Mycobacterium peregrinum_A	87.9972	1562	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_002102345.1	s__Mycobacterium peregrinum	87.9053	1605	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	-
GCF_000455325.1	s__Mycobacterium septicum	87.7285	1618	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_004762045.1	s__Mycobacterium sp004762045	87.5508	1579	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_001245615.1	s__Mycobacterium neworleansense	86.9602	1554	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_002086835.1	s__Mycobacterium porcinum	86.5529	1511	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001942625.1	s__Mycobacterium syngnathidarum	86.4993	1580	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_001942045.1	s__Mycobacterium porcinum_A	86.496	1471	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_000723385.1	s__Mycobacterium farcinogenes	85.9561	1511	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_900078665.2	s__Mycobacterium houstonense	85.4498	1471	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_002157835.1	s__Mycobacterium dioxanotrophicus	82.2508	1295	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_001905655.1	s__Mycobacterium sp001905655	80.005	805	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_011694515.1	s__Mycobacterium sp011694515	79.3942	792	2114	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:15,823] [INFO] GTDB search result was written to GCF_017876775.1_ASM1787677v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:15,828] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:15,834] [INFO] DFAST_QC result json was written to GCF_017876775.1_ASM1787677v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:15,834] [INFO] DFAST_QC completed!
[2024-01-24 13:15:15,835] [INFO] Total running time: 0h2m25s