[2024-01-24 12:37:37,927] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:37,929] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:37,929] [INFO] DQC Reference Directory: /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference
[2024-01-24 12:37:41,017] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:41,018] [INFO] Task started: Prodigal
[2024-01-24 12:37:41,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a995553-8166-49d9-ac75-4bb33c79a377/GCF_022179545.1_ASM2217954v1_genomic.fna.gz | prodigal -d GCF_022179545.1_ASM2217954v1_genomic.fna/cds.fna -a GCF_022179545.1_ASM2217954v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:38:03,639] [INFO] Task succeeded: Prodigal
[2024-01-24 12:38:03,639] [INFO] Task started: HMMsearch
[2024-01-24 12:38:03,639] [INFO] Running command: hmmsearch --tblout GCF_022179545.1_ASM2217954v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/reference_markers.hmm GCF_022179545.1_ASM2217954v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:38:03,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:38:03,992] [INFO] Found 6/6 markers.
[2024-01-24 12:38:04,054] [INFO] Query marker FASTA was written to GCF_022179545.1_ASM2217954v1_genomic.fna/markers.fasta
[2024-01-24 12:38:04,054] [INFO] Task started: Blastn
[2024-01-24 12:38:04,054] [INFO] Running command: blastn -query GCF_022179545.1_ASM2217954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/reference_markers.fasta -out GCF_022179545.1_ASM2217954v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:05,307] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:05,311] [INFO] Selected 15 target genomes.
[2024-01-24 12:38:05,311] [INFO] Target genome list was writen to GCF_022179545.1_ASM2217954v1_genomic.fna/target_genomes.txt
[2024-01-24 12:38:05,360] [INFO] Task started: fastANI
[2024-01-24 12:38:05,360] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a995553-8166-49d9-ac75-4bb33c79a377/GCF_022179545.1_ASM2217954v1_genomic.fna.gz --refList GCF_022179545.1_ASM2217954v1_genomic.fna/target_genomes.txt --output GCF_022179545.1_ASM2217954v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:29,553] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:29,553] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:29,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:29,567] [INFO] Found 15 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:38:29,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:38:29,567] [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=JCM 6387	GCA_022179545.1	144549	1766	type	True	100.0	2126	2135	95	conclusive
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	99.9365	2053	2135	95	conclusive
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	98.7619	1947	2135	95	conclusive
Mycolicibacterium peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	88.1044	1729	2135	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	87.1228	1656	2135	95	below_threshold
Mycolicibacterium boenickei	strain=JCM 15653	GCA_010731295.1	146017	146017	type	True	87.0645	1691	2135	95	below_threshold
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	87.0227	1672	2135	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	86.9718	1692	2135	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	86.8357	1700	2135	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	86.3504	1489	2135	95	below_threshold
Mycolicibacterium houstonense	strain=type strain: ATCC 49403	GCA_900078665.2	146021	146021	type	True	85.9387	1666	2135	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.5472	849	2135	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.4574	813	2135	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4453	854	2135	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.3399	846	2135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:29,569] [INFO] DFAST Taxonomy check result was written to GCF_022179545.1_ASM2217954v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:29,570] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:29,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:29,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/checkm_data
[2024-01-24 12:38:29,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:29,633] [INFO] Task started: CheckM
[2024-01-24 12:38:29,634] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022179545.1_ASM2217954v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022179545.1_ASM2217954v1_genomic.fna/checkm_input GCF_022179545.1_ASM2217954v1_genomic.fna/checkm_result
[2024-01-24 12:39:43,353] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:43,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:43,385] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:43,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:43,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022179545.1_ASM2217954v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:43,386] [INFO] Task started: Blastn
[2024-01-24 12:39:43,386] [INFO] Running command: blastn -query GCF_022179545.1_ASM2217954v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78feb7ec-df49-48c7-bdd6-e84f4f486cf5/dqc_reference/reference_markers_gtdb.fasta -out GCF_022179545.1_ASM2217954v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:45,161] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:45,165] [INFO] Selected 14 target genomes.
[2024-01-24 12:39:45,165] [INFO] Target genome list was writen to GCF_022179545.1_ASM2217954v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:45,181] [INFO] Task started: fastANI
[2024-01-24 12:39:45,181] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a995553-8166-49d9-ac75-4bb33c79a377/GCF_022179545.1_ASM2217954v1_genomic.fna.gz --refList GCF_022179545.1_ASM2217954v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022179545.1_ASM2217954v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:40:07,735] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:07,755] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:40:07,755] [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	99.9365	2053	2135	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	88.1003	1721	2135	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	88.0962	1731	2135	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	87.9125	1760	2135	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	87.2719	1671	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.34	98.08	0.90	0.87	16	-
GCF_010731295.1	s__Mycobacterium boenickei	87.0587	1692	2135	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	87.0472	1687	2135	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	86.9974	1603	2135	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	86.9734	1692	2135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.04	95.11	0.88	0.83	8	-
GCF_010727325.1	s__Mycobacterium alvei	86.3411	1490	2135	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	86.2322	1611	2135	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	85.9333	1667	2135	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	84.8827	1422	2135	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	81.5062	1204	2135	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 12:40:07,756] [INFO] GTDB search result was written to GCF_022179545.1_ASM2217954v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:40:07,757] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:40:07,761] [INFO] DFAST_QC result json was written to GCF_022179545.1_ASM2217954v1_genomic.fna/dqc_result.json
[2024-01-24 12:40:07,762] [INFO] DFAST_QC completed!
[2024-01-24 12:40:07,762] [INFO] Total running time: 0h2m30s