[2024-01-25 20:07:50,538] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:50,541] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:50,541] [INFO] DQC Reference Directory: /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference
[2024-01-25 20:07:51,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:51,664] [INFO] Task started: Prodigal
[2024-01-25 20:07:51,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgbaa4acc4-4c20-4274-a1d4-0615fc1ab2a9/GCF_002102345.1_ASM210234v1_genomic.fna.gz | prodigal -d GCF_002102345.1_ASM210234v1_genomic.fna/cds.fna -a GCF_002102345.1_ASM210234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:08:12,108] [INFO] Task succeeded: Prodigal
[2024-01-25 20:08:12,109] [INFO] Task started: HMMsearch
[2024-01-25 20:08:12,109] [INFO] Running command: hmmsearch --tblout GCF_002102345.1_ASM210234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/reference_markers.hmm GCF_002102345.1_ASM210234v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:08:12,437] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:08:12,438] [INFO] Found 6/6 markers.
[2024-01-25 20:08:12,499] [INFO] Query marker FASTA was written to GCF_002102345.1_ASM210234v1_genomic.fna/markers.fasta
[2024-01-25 20:08:12,499] [INFO] Task started: Blastn
[2024-01-25 20:08:12,499] [INFO] Running command: blastn -query GCF_002102345.1_ASM210234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/reference_markers.fasta -out GCF_002102345.1_ASM210234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:13,679] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:13,681] [INFO] Selected 14 target genomes.
[2024-01-25 20:08:13,682] [INFO] Target genome list was writen to GCF_002102345.1_ASM210234v1_genomic.fna/target_genomes.txt
[2024-01-25 20:08:13,710] [INFO] Task started: fastANI
[2024-01-25 20:08:13,710] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa4acc4-4c20-4274-a1d4-0615fc1ab2a9/GCF_002102345.1_ASM210234v1_genomic.fna.gz --refList GCF_002102345.1_ASM210234v1_genomic.fna/target_genomes.txt --output GCF_002102345.1_ASM210234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:08:35,422] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:35,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:08:35,423] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:08:35,432] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:08:35,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:08:35,433] [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 peregrinum	strain=DSM 43271	GCA_002102345.1	43304	43304	type	True	100.0	2311	2313	95	conclusive
Mycolicibacterium septicum	strain=ATCC 700731	GCA_012396425.1	98668	98668	type	True	88.2159	1787	2313	95	below_threshold
Mycolicibacterium septicum	strain=type strain: DSM 44393	GCA_000455325.1	98668	98668	type	True	88.1995	1796	2313	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=DSM 46621	GCA_000295855.1	144549	1766	type	True	87.9997	1738	2313	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	87.9913	1751	2313	95	below_threshold
Mycolicibacterium nivoides	strain=DL90	GCA_003855255.1	2487344	2487344	type	True	87.8597	1792	2313	95	below_threshold
Mycolicibacterium fortuitum subsp. acetamidolyticum	strain=JCM6368	GCA_001570465.1	144550	1766	type	True	87.8448	1819	2313	95	below_threshold
Mycolicibacterium lutetiense	strain=DSM 46713	GCA_017876775.1	1641992	1641992	type	True	87.8385	1604	2313	95	below_threshold
Mycolicibacterium alvei	strain=JCM 12272	GCA_010727325.1	67081	67081	type	True	87.6986	1568	2313	95	below_threshold
Mycolicibacterium conceptionense	strain=CCUG 50187	GCA_002102065.1	451644	451644	suspected-type	True	86.9778	1697	2313	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.4996	881	2313	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.299	851	2313	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	79.2784	899	2313	95	below_threshold
Mycolicibacterium stellerae	strain=CECT 8783	GCA_003719305.1	2358193	2358193	type	True	79.0602	867	2313	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:08:35,435] [INFO] DFAST Taxonomy check result was written to GCF_002102345.1_ASM210234v1_genomic.fna/tc_result.tsv
[2024-01-25 20:08:35,435] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:08:35,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:08:35,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/checkm_data
[2024-01-25 20:08:35,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:08:35,501] [INFO] Task started: CheckM
[2024-01-25 20:08:35,501] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002102345.1_ASM210234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002102345.1_ASM210234v1_genomic.fna/checkm_input GCF_002102345.1_ASM210234v1_genomic.fna/checkm_result
[2024-01-25 20:09:43,210] [INFO] Task succeeded: CheckM
[2024-01-25 20:09:43,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:09:43,229] [INFO] ===== Completeness check finished =====
[2024-01-25 20:09:43,229] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:09:43,230] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002102345.1_ASM210234v1_genomic.fna/markers.fasta)
[2024-01-25 20:09:43,230] [INFO] Task started: Blastn
[2024-01-25 20:09:43,231] [INFO] Running command: blastn -query GCF_002102345.1_ASM210234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg736d1459-51d9-40b6-92bd-214ffd01b56a/dqc_reference/reference_markers_gtdb.fasta -out GCF_002102345.1_ASM210234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:09:44,881] [INFO] Task succeeded: Blastn
[2024-01-25 20:09:44,883] [INFO] Selected 10 target genomes.
[2024-01-25 20:09:44,883] [INFO] Target genome list was writen to GCF_002102345.1_ASM210234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:09:44,899] [INFO] Task started: fastANI
[2024-01-25 20:09:44,899] [INFO] Running command: fastANI --query /var/lib/cwl/stgbaa4acc4-4c20-4274-a1d4-0615fc1ab2a9/GCF_002102345.1_ASM210234v1_genomic.fna.gz --refList GCF_002102345.1_ASM210234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002102345.1_ASM210234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:10:01,385] [INFO] Task succeeded: fastANI
[2024-01-25 20:10:01,392] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:10:01,392] [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_002102345.1	s__Mycobacterium peregrinum	100.0	2311	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	98.27	0.94	0.91	5	conclusive
GCF_001665625.1	s__Mycobacterium peregrinum_B	94.2696	1832	2313	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	93.8827	1872	2313	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	88.9487	1779	2313	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	88.1903	1797	2313	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	87.9983	1738	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.13	96.41	0.93	0.89	30	-
GCF_017876775.1	s__Mycobacterium lutetiense	87.8413	1604	2313	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	87.7072	1567	2313	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	87.6688	1720	2313	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	86.7225	1616	2313	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.38	97.86	0.91	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-25 20:10:01,393] [INFO] GTDB search result was written to GCF_002102345.1_ASM210234v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:10:01,394] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:10:01,396] [INFO] DFAST_QC result json was written to GCF_002102345.1_ASM210234v1_genomic.fna/dqc_result.json
[2024-01-25 20:10:01,396] [INFO] DFAST_QC completed!
[2024-01-25 20:10:01,397] [INFO] Total running time: 0h2m11s