[2024-01-25 17:38:05,551] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:05,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:05,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference
[2024-01-25 17:38:06,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:06,730] [INFO] Task started: Prodigal
[2024-01-25 17:38:06,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg42aea33f-fd58-4949-bdb4-55c0c866f1c3/GCF_026013605.1_ASM2601360v1_genomic.fna.gz | prodigal -d GCF_026013605.1_ASM2601360v1_genomic.fna/cds.fna -a GCF_026013605.1_ASM2601360v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:24,478] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:24,479] [INFO] Task started: HMMsearch
[2024-01-25 17:38:24,479] [INFO] Running command: hmmsearch --tblout GCF_026013605.1_ASM2601360v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/reference_markers.hmm GCF_026013605.1_ASM2601360v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:24,801] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:24,802] [INFO] Found 6/6 markers.
[2024-01-25 17:38:24,852] [INFO] Query marker FASTA was written to GCF_026013605.1_ASM2601360v1_genomic.fna/markers.fasta
[2024-01-25 17:38:24,853] [INFO] Task started: Blastn
[2024-01-25 17:38:24,853] [INFO] Running command: blastn -query GCF_026013605.1_ASM2601360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/reference_markers.fasta -out GCF_026013605.1_ASM2601360v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:25,483] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:25,486] [INFO] Selected 21 target genomes.
[2024-01-25 17:38:25,486] [INFO] Target genome list was writen to GCF_026013605.1_ASM2601360v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:25,492] [INFO] Task started: fastANI
[2024-01-25 17:38:25,492] [INFO] Running command: fastANI --query /var/lib/cwl/stg42aea33f-fd58-4949-bdb4-55c0c866f1c3/GCF_026013605.1_ASM2601360v1_genomic.fna.gz --refList GCF_026013605.1_ASM2601360v1_genomic.fna/target_genomes.txt --output GCF_026013605.1_ASM2601360v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:40,668] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:40,668] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:40,668] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:40,675] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:38:40,675] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:38:40,675] [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
Labilibacter sediminis	strain=CG51	GCA_005877885.1	2570926	2570926	type	True	78.1696	290	2048	95	below_threshold
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	77.991	280	2048	95	below_threshold
Carboxylicivirga sediminis	strain=JR1	GCA_018156225.1	2006564	2006564	type	True	77.7537	98	2048	95	below_threshold
Saccharicrinis fermentans	strain=JCM 21142	GCA_000583675.1	982	982	type	True	77.6445	223	2048	95	below_threshold
Saccharicrinis fermentans	strain=DSM 9555	GCA_000517085.1	982	982	type	True	77.6419	229	2048	95	below_threshold
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	77.3398	220	2048	95	below_threshold
Carboxylicivirga mesophila	strain=JCM 18290	GCA_018271975.1	1166478	1166478	type	True	76.5727	81	2048	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:40,676] [INFO] DFAST Taxonomy check result was written to GCF_026013605.1_ASM2601360v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:40,677] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:40,677] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:40,677] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/checkm_data
[2024-01-25 17:38:40,678] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:40,741] [INFO] Task started: CheckM
[2024-01-25 17:38:40,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026013605.1_ASM2601360v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026013605.1_ASM2601360v1_genomic.fna/checkm_input GCF_026013605.1_ASM2601360v1_genomic.fna/checkm_result
[2024-01-25 17:39:31,885] [INFO] Task succeeded: CheckM
[2024-01-25 17:39:31,886] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:39:31,906] [INFO] ===== Completeness check finished =====
[2024-01-25 17:39:31,906] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:39:31,907] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026013605.1_ASM2601360v1_genomic.fna/markers.fasta)
[2024-01-25 17:39:31,907] [INFO] Task started: Blastn
[2024-01-25 17:39:31,907] [INFO] Running command: blastn -query GCF_026013605.1_ASM2601360v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg33ce7185-8ca7-4471-a408-e2fcc460eec7/dqc_reference/reference_markers_gtdb.fasta -out GCF_026013605.1_ASM2601360v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:32,859] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:32,864] [INFO] Selected 24 target genomes.
[2024-01-25 17:39:32,864] [INFO] Target genome list was writen to GCF_026013605.1_ASM2601360v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:39:32,891] [INFO] Task started: fastANI
[2024-01-25 17:39:32,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg42aea33f-fd58-4949-bdb4-55c0c866f1c3/GCF_026013605.1_ASM2601360v1_genomic.fna.gz --refList GCF_026013605.1_ASM2601360v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026013605.1_ASM2601360v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:39:49,672] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:49,680] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 17:39:49,680] [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_005877885.1	s__Saccharicrinis sediminis	78.1647	291	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271995.1	s__Carboxylicivirga linearis	78.1062	184	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001659685.2	s__Saccharicrinis marinus	77.991	280	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018156225.1	s__Carboxylicivirga sediminis	77.7987	99	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000517085.1	s__Saccharicrinis fermentans	77.6419	229	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001660705.2	s__Saccharicrinis aurantiacus	77.3299	219	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271975.1	s__Carboxylicivirga mesophila	76.5727	81	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097485.1	s__Carboxylicivirga sp007097485	76.1362	103	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002429115.1	s__Carboxylicivirga sp002429115	76.0221	65	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342685.1	s__UBA12077 sp016342685	75.2398	67	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001769005.1	s__UBA12077 sp001769005	74.948	62	2048	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA12077;g__UBA12077	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:39:49,682] [INFO] GTDB search result was written to GCF_026013605.1_ASM2601360v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:39:49,682] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:39:49,686] [INFO] DFAST_QC result json was written to GCF_026013605.1_ASM2601360v1_genomic.fna/dqc_result.json
[2024-01-25 17:39:49,686] [INFO] DFAST_QC completed!
[2024-01-25 17:39:49,686] [INFO] Total running time: 0h1m44s