[2024-01-24 13:17:27,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:27,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:27,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference
[2024-01-24 13:17:28,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:28,294] [INFO] Task started: Prodigal
[2024-01-24 13:17:28,294] [INFO] Running command: gunzip -c /var/lib/cwl/stgcdb2089b-f5d7-40d7-ba99-88b5949ef3e3/GCF_000379765.1_ASM37976v1_genomic.fna.gz | prodigal -d GCF_000379765.1_ASM37976v1_genomic.fna/cds.fna -a GCF_000379765.1_ASM37976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:03,972] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:03,972] [INFO] Task started: HMMsearch
[2024-01-24 13:18:03,973] [INFO] Running command: hmmsearch --tblout GCF_000379765.1_ASM37976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/reference_markers.hmm GCF_000379765.1_ASM37976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:04,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:04,350] [INFO] Found 6/6 markers.
[2024-01-24 13:18:04,426] [INFO] Query marker FASTA was written to GCF_000379765.1_ASM37976v1_genomic.fna/markers.fasta
[2024-01-24 13:18:04,427] [INFO] Task started: Blastn
[2024-01-24 13:18:04,427] [INFO] Running command: blastn -query GCF_000379765.1_ASM37976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/reference_markers.fasta -out GCF_000379765.1_ASM37976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:05,014] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:05,017] [INFO] Selected 23 target genomes.
[2024-01-24 13:18:05,018] [INFO] Target genome list was writen to GCF_000379765.1_ASM37976v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:05,048] [INFO] Task started: fastANI
[2024-01-24 13:18:05,048] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb2089b-f5d7-40d7-ba99-88b5949ef3e3/GCF_000379765.1_ASM37976v1_genomic.fna.gz --refList GCF_000379765.1_ASM37976v1_genomic.fna/target_genomes.txt --output GCF_000379765.1_ASM37976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:24,825] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:24,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:24,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:24,834] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:24,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:24,835] [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
Flexithrix dorotheae	strain=DSM 6795	GCA_000379765.1	70993	70993	type	True	100.0	3124	3132	95	conclusive
Polaribacter filamentus	strain=ATCC 700397	GCA_002943715.1	53483	53483	type	True	75.6759	50	3132	95	below_threshold
Sediminitomix flava	strain=DSM 28229	GCA_003149185.1	379075	379075	type	True	75.2941	58	3132	95	below_threshold
Flammeovirga pacifica	strain=WPAGA1	GCA_000807855.2	915059	915059	type	True	75.1555	66	3132	95	below_threshold
Cyclobacterium qasimii	strain=M12-11B	GCA_000427295.1	1350429	1350429	type	True	75.0521	55	3132	95	below_threshold
Cyclobacterium qasimii	strain=NBRC 106168	GCA_007991695.1	1350429	1350429	type	True	75.0416	56	3132	95	below_threshold
Flammeovirga aprica	strain=ATCC 23126	GCA_012844305.1	29528	29528	type	True	74.8414	73	3132	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:24,838] [INFO] DFAST Taxonomy check result was written to GCF_000379765.1_ASM37976v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:24,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:24,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:24,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/checkm_data
[2024-01-24 13:18:24,845] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:24,939] [INFO] Task started: CheckM
[2024-01-24 13:18:24,940] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000379765.1_ASM37976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000379765.1_ASM37976v1_genomic.fna/checkm_input GCF_000379765.1_ASM37976v1_genomic.fna/checkm_result
[2024-01-24 13:20:04,736] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:04,738] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:04,761] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:04,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:04,762] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000379765.1_ASM37976v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:04,762] [INFO] Task started: Blastn
[2024-01-24 13:20:04,762] [INFO] Running command: blastn -query GCF_000379765.1_ASM37976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40b2b7bc-2814-47b9-8bea-617f6dceebed/dqc_reference/reference_markers_gtdb.fasta -out GCF_000379765.1_ASM37976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:05,553] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:05,556] [INFO] Selected 28 target genomes.
[2024-01-24 13:20:05,556] [INFO] Target genome list was writen to GCF_000379765.1_ASM37976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:05,602] [INFO] Task started: fastANI
[2024-01-24 13:20:05,602] [INFO] Running command: fastANI --query /var/lib/cwl/stgcdb2089b-f5d7-40d7-ba99-88b5949ef3e3/GCF_000379765.1_ASM37976v1_genomic.fna.gz --refList GCF_000379765.1_ASM37976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000379765.1_ASM37976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:30,786] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:30,797] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:30,798] [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_000379765.1	s__Flexithrix dorotheae	100.0	3123	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flexithrix	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002729595.1	s__GCA-2729595 sp002729595	75.7679	110	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__GCA-2729595	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015533855.1	s__Echinicola sp015533855	75.6416	57	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Echinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050135.1	s__Cyclobacterium amurskyense	75.4617	63	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149185.1	s__Sediminitomix flava	75.2941	58	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Sediminitomix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000807855.2	s__Flammeovirga pacifica	75.1555	66	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427295.1	s__Cyclobacterium qasimii	75.0521	55	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Cyclobacterium	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001583495.1	s__Flammeovirga sp001583495	75.0155	77	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Flammeovirgaceae;g__Flammeovirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009801115.1	s__Dyadobacter sp009801115	74.9663	52	3132	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:30,800] [INFO] GTDB search result was written to GCF_000379765.1_ASM37976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:30,800] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:30,803] [INFO] DFAST_QC result json was written to GCF_000379765.1_ASM37976v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:30,803] [INFO] DFAST_QC completed!
[2024-01-24 13:20:30,803] [INFO] Total running time: 0h3m4s