[2024-01-24 15:27:02,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:02,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:02,686] [INFO] DQC Reference Directory: /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference
[2024-01-24 15:27:03,886] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:03,886] [INFO] Task started: Prodigal
[2024-01-24 15:27:03,887] [INFO] Running command: gunzip -c /var/lib/cwl/stgebfb4a51-fe6a-4603-ac5f-99e48d200d36/GCF_025821225.1_ASM2582122v1_genomic.fna.gz | prodigal -d GCF_025821225.1_ASM2582122v1_genomic.fna/cds.fna -a GCF_025821225.1_ASM2582122v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:15,755] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:15,755] [INFO] Task started: HMMsearch
[2024-01-24 15:27:15,755] [INFO] Running command: hmmsearch --tblout GCF_025821225.1_ASM2582122v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/reference_markers.hmm GCF_025821225.1_ASM2582122v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:16,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:16,011] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgebfb4a51-fe6a-4603-ac5f-99e48d200d36/GCF_025821225.1_ASM2582122v1_genomic.fna.gz]
[2024-01-24 15:27:16,059] [INFO] Query marker FASTA was written to GCF_025821225.1_ASM2582122v1_genomic.fna/markers.fasta
[2024-01-24 15:27:16,059] [INFO] Task started: Blastn
[2024-01-24 15:27:16,059] [INFO] Running command: blastn -query GCF_025821225.1_ASM2582122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/reference_markers.fasta -out GCF_025821225.1_ASM2582122v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:17,253] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:17,256] [INFO] Selected 9 target genomes.
[2024-01-24 15:27:17,257] [INFO] Target genome list was writen to GCF_025821225.1_ASM2582122v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:17,262] [INFO] Task started: fastANI
[2024-01-24 15:27:17,262] [INFO] Running command: fastANI --query /var/lib/cwl/stgebfb4a51-fe6a-4603-ac5f-99e48d200d36/GCF_025821225.1_ASM2582122v1_genomic.fna.gz --refList GCF_025821225.1_ASM2582122v1_genomic.fna/target_genomes.txt --output GCF_025821225.1_ASM2582122v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:26,460] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:26,461] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:26,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:26,471] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:26,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:26,472] [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 insubricum	strain=JCM 16366	GCA_010731615.1	444597	444597	type	True	99.8743	1192	1203	95	conclusive
Mycolicibacterium fallax	strain=DSM 44179	GCA_002101995.1	1793	1793	type	True	84.1649	799	1203	95	below_threshold
Mycolicibacterium fallax	strain=JCM 6405	GCA_010726955.1	1793	1793	type	True	84.1339	823	1203	95	below_threshold
Mycolicibacterium brumae	strain=DSM 44177	GCA_004014795.1	85968	85968	type	True	82.7867	650	1203	95	below_threshold
Mycolicibacterium brumae	strain=ATCC 51384	GCA_025215495.1	85968	85968	type	True	82.6972	664	1203	95	below_threshold
Mycolicibacterium chitae	strain=NCTC10485	GCA_900637205.1	1792	1792	type	True	81.2217	678	1203	95	below_threshold
Mycolicibacterium chitae	strain=JCM 12403	GCA_010727725.1	1792	1792	type	True	81.1288	691	1203	95	below_threshold
Mycolicibacterium mageritense	strain=CIP 104973	GCA_000612825.1	53462	53462	type	True	79.7583	590	1203	95	below_threshold
Mycolicibacterium mageritense	strain=JCM 12375	GCA_010727475.1	53462	53462	type	True	79.7042	601	1203	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:26,474] [INFO] DFAST Taxonomy check result was written to GCF_025821225.1_ASM2582122v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:26,475] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:26,475] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:26,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/checkm_data
[2024-01-24 15:27:26,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:26,528] [INFO] Task started: CheckM
[2024-01-24 15:27:26,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821225.1_ASM2582122v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821225.1_ASM2582122v1_genomic.fna/checkm_input GCF_025821225.1_ASM2582122v1_genomic.fna/checkm_result
[2024-01-24 15:28:06,348] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:06,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:06,369] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:06,369] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:06,370] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821225.1_ASM2582122v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:06,370] [INFO] Task started: Blastn
[2024-01-24 15:28:06,370] [INFO] Running command: blastn -query GCF_025821225.1_ASM2582122v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga1cc4a35-6377-4c65-bda1-0577678957a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821225.1_ASM2582122v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:08,034] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:08,038] [INFO] Selected 15 target genomes.
[2024-01-24 15:28:08,038] [INFO] Target genome list was writen to GCF_025821225.1_ASM2582122v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:08,059] [INFO] Task started: fastANI
[2024-01-24 15:28:08,059] [INFO] Running command: fastANI --query /var/lib/cwl/stgebfb4a51-fe6a-4603-ac5f-99e48d200d36/GCF_025821225.1_ASM2582122v1_genomic.fna.gz --refList GCF_025821225.1_ASM2582122v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821225.1_ASM2582122v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:24,111] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:24,127] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:24,127] [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_010731615.1	s__Mycobacterium insubricum	99.8743	1192	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_010726955.1	s__Mycobacterium fallax	84.1165	824	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.97	0.97	2	-
GCF_004014795.1	s__Mycobacterium brumae	82.8384	646	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.98	0.98	0.98	3	-
GCF_900637205.1	s__Mycobacterium chitae	81.2237	677	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001668625.1	s__Mycobacterium sp001668625	80.6445	533	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018455725.1	s__Mycobacterium sp018455725	80.3704	530	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019050325.1	s__Mycobacterium fortunisiensis	80.2867	641	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667265.1	s__Mycobacterium sp001667265	80.1743	620	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001722335.1	s__Mycobacterium flavescens_A	80.1441	605	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002723835.1	s__Mycobacterium sp002723835	79.9885	607	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317305.3	s__Mycobacterium neoaurum_A	79.8352	517	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.30	95.79	0.98	0.90	7	-
GCF_001665535.1	s__Mycobacterium sp001665535	79.8122	511	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.97	96.97	0.90	0.90	2	-
GCF_010730955.1	s__Mycobacterium aubagnense	79.7628	568	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_010727475.1	s__Mycobacterium mageritense	79.6982	603	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.88	98.33	0.91	0.85	5	-
GCF_001570425.1	s__Mycobacterium brisbanense	79.6853	596	1203	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.59	97.59	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:24,129] [INFO] GTDB search result was written to GCF_025821225.1_ASM2582122v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:24,129] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:24,132] [INFO] DFAST_QC result json was written to GCF_025821225.1_ASM2582122v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:24,133] [INFO] DFAST_QC completed!
[2024-01-24 15:28:24,133] [INFO] Total running time: 0h1m21s