[2023-06-28 03:04:45,071] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:04:45,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:04:45,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference
[2023-06-28 03:04:47,367] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:04:47,368] [INFO] Task started: Prodigal
[2023-06-28 03:04:47,368] [INFO] Running command: gunzip -c /var/lib/cwl/stge70fecc7-72e5-42c2-9bd2-bd19876c5b17/GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:05:02,916] [INFO] Task succeeded: Prodigal
[2023-06-28 03:05:02,916] [INFO] Task started: HMMsearch
[2023-06-28 03:05:02,917] [INFO] Running command: hmmsearch --tblout GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/reference_markers.hmm GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:05:03,171] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:05:03,172] [INFO] Found 6/6 markers.
[2023-06-28 03:05:03,208] [INFO] Query marker FASTA was written to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 03:05:03,208] [INFO] Task started: Blastn
[2023-06-28 03:05:03,209] [INFO] Running command: blastn -query GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/reference_markers.fasta -out GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:05:03,820] [INFO] Task succeeded: Blastn
[2023-06-28 03:05:03,826] [INFO] Selected 22 target genomes.
[2023-06-28 03:05:03,827] [INFO] Target genome list was writen to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 03:05:03,835] [INFO] Task started: fastANI
[2023-06-28 03:05:03,835] [INFO] Running command: fastANI --query /var/lib/cwl/stge70fecc7-72e5-42c2-9bd2-bd19876c5b17/GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:05:16,407] [INFO] Task succeeded: fastANI
[2023-06-28 03:05:16,408] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:05:16,409] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:05:16,417] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:05:16,417] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 03:05:16,417] [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
Crocinitomix catalasitica	strain=ATCC 23190	GCA_000621625.1	184607	184607	type	True	76.5529	122	1338	95	below_threshold
Crocinitomix algicola	strain=0182	GCA_001661595.2	1740263	1740263	type	True	76.3162	91	1338	95	below_threshold
Putridiphycobacter roseus	strain=SM1701	GCA_003234935.1	2219161	2219161	type	True	76.1674	86	1338	95	below_threshold
Brumimicrobium glaciale	strain=IC156	GCA_004152935.1	200475	200475	type	True	76.1384	58	1338	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 03:05:16,419] [INFO] DFAST Taxonomy check result was written to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 03:05:16,420] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:05:16,420] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:05:16,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/checkm_data
[2023-06-28 03:05:16,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:05:16,470] [INFO] Task started: CheckM
[2023-06-28 03:05:16,470] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 03:06:06,218] [INFO] Task succeeded: CheckM
[2023-06-28 03:06:06,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:06:06,242] [INFO] ===== Completeness check finished =====
[2023-06-28 03:06:06,242] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:06:06,243] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 03:06:06,243] [INFO] Task started: Blastn
[2023-06-28 03:06:06,243] [INFO] Running command: blastn -query GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg2877df45-9f29-4eae-8670-472dbf2cad5a/dqc_reference/reference_markers_gtdb.fasta -out GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:06:07,041] [INFO] Task succeeded: Blastn
[2023-06-28 03:06:07,047] [INFO] Selected 25 target genomes.
[2023-06-28 03:06:07,047] [INFO] Target genome list was writen to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:06:07,062] [INFO] Task started: fastANI
[2023-06-28 03:06:07,062] [INFO] Running command: fastANI --query /var/lib/cwl/stge70fecc7-72e5-42c2-9bd2-bd19876c5b17/GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:06:20,018] [INFO] Task succeeded: fastANI
[2023-06-28 03:06:20,030] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:06:20,031] [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
GCA_905478225.1	s__Crocinitomix sp905478225	76.777	126	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013138735.1	s__Crocinitomix sp013138735	76.7752	120	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762645.1	s__JABURP01 sp014762645	76.6456	125	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JABURP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621625.1	s__Crocinitomix catalasitica	76.5529	122	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661595.2	s__Crocinitomix algicola	76.3162	91	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Crocinitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003234935.1	s__Putridiphycobacter roseus	76.1674	86	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Putridiphycobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152935.1	s__Brumimicrobium glaciale	76.1384	58	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__Brumimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016178305.1	s__CAIUKX01 sp016178305	75.7237	54	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__CAIUKX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016708105.1	s__JADJGJ01 sp016708105	75.3956	59	1338	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__JADJGJ01	95.0	99.76	99.76	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-28 03:06:20,033] [INFO] GTDB search result was written to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 03:06:20,033] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:06:20,037] [INFO] DFAST_QC result json was written to GCA_913054135.1_SRR3646399_bin.2_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 03:06:20,038] [INFO] DFAST_QC completed!
[2023-06-28 03:06:20,038] [INFO] Total running time: 0h1m35s