[2024-01-24 13:37:05,016] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,020] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,022] [INFO] DQC Reference Directory: /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference
[2024-01-24 13:37:06,466] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,467] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,467] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfeab35f-6b2d-439c-bcbc-c459907ff4fa/GCF_031458155.1_ASM3145815v1_genomic.fna.gz | prodigal -d GCF_031458155.1_ASM3145815v1_genomic.fna/cds.fna -a GCF_031458155.1_ASM3145815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:39,879] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:39,879] [INFO] Task started: HMMsearch
[2024-01-24 13:37:39,879] [INFO] Running command: hmmsearch --tblout GCF_031458155.1_ASM3145815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/reference_markers.hmm GCF_031458155.1_ASM3145815v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:40,296] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:40,297] [INFO] Found 6/6 markers.
[2024-01-24 13:37:40,373] [INFO] Query marker FASTA was written to GCF_031458155.1_ASM3145815v1_genomic.fna/markers.fasta
[2024-01-24 13:37:40,374] [INFO] Task started: Blastn
[2024-01-24 13:37:40,374] [INFO] Running command: blastn -query GCF_031458155.1_ASM3145815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/reference_markers.fasta -out GCF_031458155.1_ASM3145815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:41,656] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:41,659] [INFO] Selected 16 target genomes.
[2024-01-24 13:37:41,660] [INFO] Target genome list was writen to GCF_031458155.1_ASM3145815v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:41,674] [INFO] Task started: fastANI
[2024-01-24 13:37:41,675] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfeab35f-6b2d-439c-bcbc-c459907ff4fa/GCF_031458155.1_ASM3145815v1_genomic.fna.gz --refList GCF_031458155.1_ASM3145815v1_genomic.fna/target_genomes.txt --output GCF_031458155.1_ASM3145815v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:38:07,485] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:07,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:38:07,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:38:07,499] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:38:07,500] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:38:07,500] [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 conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	98.2754	1853	2028	95	conclusive
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	88.373	1655	2028	95	below_threshold
Mycolicibacterium neworleansense	strain=type strain: ATCC 49404	GCA_001245615.1	146018	146018	type	True	87.595	1686	2028	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	87.5495	1632	2028	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	87.5283	1659	2028	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	87.4807	1647	2028	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	87.2825	1638	2028	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	87.2258	1635	2028	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	87.2214	1670	2028	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	86.044	1564	2028	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	85.8773	1506	2028	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	85.8771	1439	2028	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.774	835	2028	95	below_threshold
Mycolicibacterium lacusdiani	strain=JXJ CY 35	GCA_021916785.1	2895283	2895283	type	True	79.705	909	2028	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.6545	850	2028	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4125	834	2028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:38:07,501] [INFO] DFAST Taxonomy check result was written to GCF_031458155.1_ASM3145815v1_genomic.fna/tc_result.tsv
[2024-01-24 13:38:07,502] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:38:07,502] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:38:07,502] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/checkm_data
[2024-01-24 13:38:07,503] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:38:07,564] [INFO] Task started: CheckM
[2024-01-24 13:38:07,564] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031458155.1_ASM3145815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031458155.1_ASM3145815v1_genomic.fna/checkm_input GCF_031458155.1_ASM3145815v1_genomic.fna/checkm_result
[2024-01-24 13:39:33,627] [INFO] Task succeeded: CheckM
[2024-01-24 13:39:33,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:39:33,651] [INFO] ===== Completeness check finished =====
[2024-01-24 13:39:33,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:39:33,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031458155.1_ASM3145815v1_genomic.fna/markers.fasta)
[2024-01-24 13:39:33,653] [INFO] Task started: Blastn
[2024-01-24 13:39:33,653] [INFO] Running command: blastn -query GCF_031458155.1_ASM3145815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg61413265-b694-4b4f-88c0-e14e05e287c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_031458155.1_ASM3145815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:39:35,447] [INFO] Task succeeded: Blastn
[2024-01-24 13:39:35,451] [INFO] Selected 15 target genomes.
[2024-01-24 13:39:35,452] [INFO] Target genome list was writen to GCF_031458155.1_ASM3145815v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:39:35,491] [INFO] Task started: fastANI
[2024-01-24 13:39:35,492] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfeab35f-6b2d-439c-bcbc-c459907ff4fa/GCF_031458155.1_ASM3145815v1_genomic.fna.gz --refList GCF_031458155.1_ASM3145815v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031458155.1_ASM3145815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:59,046] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:59,060] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:39:59,060] [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_000723385.1	s__Mycobacterium farcinogenes	99.9454	2013	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	conclusive
GCF_001942625.1	s__Mycobacterium syngnathidarum	89.2218	1592	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
GCF_010731295.1	s__Mycobacterium boenickei	88.3813	1654	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.96	1.00	1.00	3	-
GCF_002086835.1	s__Mycobacterium porcinum	88.1503	1670	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.47	97.32	0.92	0.87	9	-
GCF_001942045.1	s__Mycobacterium porcinum_A	88.0539	1582	2028	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	87.5986	1683	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455325.1	s__Mycobacterium septicum	87.539	1658	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_000295855.1	s__Mycobacterium fortuitum	87.2685	1640	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_000426065.1	s__Mycobacterium sp000426065	86.4888	1617	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078665.2	s__Mycobacterium houstonense	86.0234	1567	2028	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	85.9064	1488	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.96	1.00	1.00	6	-
GCF_010727325.1	s__Mycobacterium alvei	85.8759	1439	2028	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	85.156	1456	2028	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	85.1443	1448	2028	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.19	98.19	0.92	0.92	2	-
GCF_000382405.1	s__Mycobacterium sp000382405	81.2254	875	2028	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 13:39:59,062] [INFO] GTDB search result was written to GCF_031458155.1_ASM3145815v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:59,063] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:59,067] [INFO] DFAST_QC result json was written to GCF_031458155.1_ASM3145815v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:59,067] [INFO] DFAST_QC completed!
[2024-01-24 13:39:59,067] [INFO] Total running time: 0h2m54s