[2024-01-25 19:03:50,500] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:03:50,502] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:03:50,502] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference
[2024-01-25 19:03:51,643] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:03:51,644] [INFO] Task started: Prodigal
[2024-01-25 19:03:51,644] [INFO] Running command: gunzip -c /var/lib/cwl/stg49800228-e2b5-4943-ba93-b7adb51c8d53/GCF_025822495.1_ASM2582249v1_genomic.fna.gz | prodigal -d GCF_025822495.1_ASM2582249v1_genomic.fna/cds.fna -a GCF_025822495.1_ASM2582249v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:04:09,947] [INFO] Task succeeded: Prodigal
[2024-01-25 19:04:09,947] [INFO] Task started: HMMsearch
[2024-01-25 19:04:09,947] [INFO] Running command: hmmsearch --tblout GCF_025822495.1_ASM2582249v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/reference_markers.hmm GCF_025822495.1_ASM2582249v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:04:10,312] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:04:10,323] [INFO] Found 6/6 markers.
[2024-01-25 19:04:10,370] [INFO] Query marker FASTA was written to GCF_025822495.1_ASM2582249v1_genomic.fna/markers.fasta
[2024-01-25 19:04:10,370] [INFO] Task started: Blastn
[2024-01-25 19:04:10,370] [INFO] Running command: blastn -query GCF_025822495.1_ASM2582249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/reference_markers.fasta -out GCF_025822495.1_ASM2582249v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:04:11,520] [INFO] Task succeeded: Blastn
[2024-01-25 19:04:11,523] [INFO] Selected 15 target genomes.
[2024-01-25 19:04:11,524] [INFO] Target genome list was writen to GCF_025822495.1_ASM2582249v1_genomic.fna/target_genomes.txt
[2024-01-25 19:04:11,534] [INFO] Task started: fastANI
[2024-01-25 19:04:11,534] [INFO] Running command: fastANI --query /var/lib/cwl/stg49800228-e2b5-4943-ba93-b7adb51c8d53/GCF_025822495.1_ASM2582249v1_genomic.fna.gz --refList GCF_025822495.1_ASM2582249v1_genomic.fna/target_genomes.txt --output GCF_025822495.1_ASM2582249v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:04:29,784] [INFO] Task succeeded: fastANI
[2024-01-25 19:04:29,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:04:29,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:04:29,795] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:04:29,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:04:29,795] [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 elephantis	strain=DSM 44368	GCA_004014805.1	81858	81858	type	True	99.989	1764	1795	95	conclusive
Mycolicibacterium pulveris	strain=JCM 6370	GCA_010725725.1	36813	36813	type	True	92.0364	1554	1795	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_001583415.1	1771	1771	type	True	82.6242	1151	1795	95	below_threshold
Mycolicibacterium phlei	strain=DSM 43239 = CCUG 21000	GCA_001582015.1	1771	1771	type	True	82.5991	1149	1795	95	below_threshold
Mycolicibacterium rutilum	strain=DSM 45405	GCA_900108565.1	370526	370526	type	True	82.5868	1164	1795	95	below_threshold
Mycolicibacterium phlei	strain=CCUG 21000	GCA_009192875.1	1771	1771	type	True	82.5795	1149	1795	95	below_threshold
Mycolicibacterium malmesburyense	strain=WCM 7299	GCA_001050015.1	1566886	1566886	type	True	82.45	1164	1795	95	below_threshold
Mycolicibacterium komanii	strain=GPK 1020	GCA_001050035.1	1566885	1566885	type	True	82.2172	1182	1795	95	below_threshold
Mycobacterium lehmannii	strain=CECT 8763	GCA_002245535.1	2048550	2048550	type	True	81.9844	1151	1795	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	81.3965	1108	1795	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	81.3943	1113	1795	95	below_threshold
Mycolicibacterium litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	80.8233	1000	1795	95	below_threshold
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	80.8191	993	1795	95	below_threshold
Mycolicibacterium gadium	strain=JCM 12688	GCA_010728925.1	1794	1794	type	True	80.5786	1057	1795	95	below_threshold
Mycobacterium helveticum	strain=16-83	GCA_007714205.1	2592811	2592811	type	True	79.5947	741	1795	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:04:29,796] [INFO] DFAST Taxonomy check result was written to GCF_025822495.1_ASM2582249v1_genomic.fna/tc_result.tsv
[2024-01-25 19:04:29,797] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:04:29,797] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:04:29,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/checkm_data
[2024-01-25 19:04:29,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:04:29,850] [INFO] Task started: CheckM
[2024-01-25 19:04:29,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822495.1_ASM2582249v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822495.1_ASM2582249v1_genomic.fna/checkm_input GCF_025822495.1_ASM2582249v1_genomic.fna/checkm_result
[2024-01-25 19:05:30,501] [INFO] Task succeeded: CheckM
[2024-01-25 19:05:30,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:05:30,516] [INFO] ===== Completeness check finished =====
[2024-01-25 19:05:30,517] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:05:30,518] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822495.1_ASM2582249v1_genomic.fna/markers.fasta)
[2024-01-25 19:05:30,518] [INFO] Task started: Blastn
[2024-01-25 19:05:30,518] [INFO] Running command: blastn -query GCF_025822495.1_ASM2582249v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1329416-b687-4f7a-bc59-e8451fb663c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822495.1_ASM2582249v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:05:32,168] [INFO] Task succeeded: Blastn
[2024-01-25 19:05:32,171] [INFO] Selected 14 target genomes.
[2024-01-25 19:05:32,171] [INFO] Target genome list was writen to GCF_025822495.1_ASM2582249v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:05:32,187] [INFO] Task started: fastANI
[2024-01-25 19:05:32,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg49800228-e2b5-4943-ba93-b7adb51c8d53/GCF_025822495.1_ASM2582249v1_genomic.fna.gz --refList GCF_025822495.1_ASM2582249v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822495.1_ASM2582249v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:05:52,151] [INFO] Task succeeded: fastANI
[2024-01-25 19:05:52,160] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:05:52,160] [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_004014805.1	s__Mycobacterium elephantis	99.989	1764	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.23	96.21	0.87	0.85	6	conclusive
GCF_010725725.1	s__Mycobacterium pulveris	92.0364	1554	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722355.1	s__Mycobacterium holsaticum	87.1193	1277	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001583415.1	s__Mycobacterium phlei	82.6224	1151	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.86	99.38	0.98	0.91	10	-
GCF_900108565.1	s__Mycobacterium rutilum	82.5503	1169	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050015.1	s__Mycobacterium malmesburyense	82.4429	1167	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500065.1	s__Mycobacterium sp001500065	82.2491	1127	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050035.1	s__Mycobacterium komanii	82.174	1188	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500025.1	s__Mycobacterium sp001500025	81.9609	1173	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	81.377	1116	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010731695.1	s__Mycobacterium litorale	80.8056	1004	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014873705.1	s__Mycobacterium sp014873705	80.6546	1038	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.28	98.28	0.92	0.92	2	-
GCF_000266905.1	s__Mycobacterium chubuense_A	80.6081	961	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010723735.1	s__Mycobacterium hippocampi_B	80.1253	955	1795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:05:52,163] [INFO] GTDB search result was written to GCF_025822495.1_ASM2582249v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:05:52,164] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:05:52,167] [INFO] DFAST_QC result json was written to GCF_025822495.1_ASM2582249v1_genomic.fna/dqc_result.json
[2024-01-25 19:05:52,167] [INFO] DFAST_QC completed!
[2024-01-25 19:05:52,167] [INFO] Total running time: 0h2m2s