[2024-01-25 18:15:35,625] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:35,627] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:35,627] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference
[2024-01-25 18:15:36,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:36,807] [INFO] Task started: Prodigal
[2024-01-25 18:15:36,807] [INFO] Running command: gunzip -c /var/lib/cwl/stg038cb3c2-65c6-492e-a0e0-3924a4489962/GCF_018271995.1_ASM1827199v1_genomic.fna.gz | prodigal -d GCF_018271995.1_ASM1827199v1_genomic.fna/cds.fna -a GCF_018271995.1_ASM1827199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:55,768] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:55,768] [INFO] Task started: HMMsearch
[2024-01-25 18:15:55,768] [INFO] Running command: hmmsearch --tblout GCF_018271995.1_ASM1827199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/reference_markers.hmm GCF_018271995.1_ASM1827199v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:56,154] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:56,155] [INFO] Found 6/6 markers.
[2024-01-25 18:15:56,206] [INFO] Query marker FASTA was written to GCF_018271995.1_ASM1827199v1_genomic.fna/markers.fasta
[2024-01-25 18:15:56,206] [INFO] Task started: Blastn
[2024-01-25 18:15:56,207] [INFO] Running command: blastn -query GCF_018271995.1_ASM1827199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/reference_markers.fasta -out GCF_018271995.1_ASM1827199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:56,852] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:56,855] [INFO] Selected 13 target genomes.
[2024-01-25 18:15:56,855] [INFO] Target genome list was writen to GCF_018271995.1_ASM1827199v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:56,867] [INFO] Task started: fastANI
[2024-01-25 18:15:56,867] [INFO] Running command: fastANI --query /var/lib/cwl/stg038cb3c2-65c6-492e-a0e0-3924a4489962/GCF_018271995.1_ASM1827199v1_genomic.fna.gz --refList GCF_018271995.1_ASM1827199v1_genomic.fna/target_genomes.txt --output GCF_018271995.1_ASM1827199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:09,011] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:09,012] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:09,012] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:09,020] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:09,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:09,020] [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
Carboxylicivirga linearis	strain=FB218	GCA_018271995.1	1628157	1628157	type	True	100.0	1950	1953	95	conclusive
Carboxylicivirga sediminis	strain=JR1	GCA_018156225.1	2006564	2006564	type	True	77.9823	231	1953	95	below_threshold
Carboxylicivirga mesophila	strain=JCM 18290	GCA_018271975.1	1166478	1166478	type	True	77.8603	208	1953	95	below_threshold
Carboxylicivirga marina	strain=N1Y132	GCA_016612505.1	2800988	2800988	type	True	77.4626	239	1953	95	below_threshold
Labilibacter marinus	strain=Y11	GCA_001659685.2	1477105	1477105	type	True	76.8763	117	1953	95	below_threshold
Saccharicrinis fermentans	strain=JCM 21142	GCA_000583675.1	982	982	type	True	76.7214	106	1953	95	below_threshold
Saccharicrinis fermentans	strain=DSM 9555	GCA_000517085.1	982	982	type	True	76.4925	109	1953	95	below_threshold
Labilibacter sediminis	strain=CG51	GCA_005877885.1	2570926	2570926	type	True	76.3683	125	1953	95	below_threshold
Saccharicrinis aurantiacus	strain=HQYD1	GCA_001660705.2	1849719	1849719	type	True	76.3529	121	1953	95	below_threshold
Draconibacterium orientale	strain=DSM 25947	GCA_900111425.1	1168034	1168034	type	True	75.9159	63	1953	95	below_threshold
Mangrovibacterium lignilyticum	strain=BM_7	GCA_010882175.1	2668052	2668052	type	True	75.8306	55	1953	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:09,022] [INFO] DFAST Taxonomy check result was written to GCF_018271995.1_ASM1827199v1_genomic.fna/tc_result.tsv
[2024-01-25 18:16:09,022] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:09,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:09,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/checkm_data
[2024-01-25 18:16:09,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:09,082] [INFO] Task started: CheckM
[2024-01-25 18:16:09,082] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018271995.1_ASM1827199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018271995.1_ASM1827199v1_genomic.fna/checkm_input GCF_018271995.1_ASM1827199v1_genomic.fna/checkm_result
[2024-01-25 18:17:03,122] [INFO] Task succeeded: CheckM
[2024-01-25 18:17:03,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:17:03,153] [INFO] ===== Completeness check finished =====
[2024-01-25 18:17:03,154] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:17:03,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018271995.1_ASM1827199v1_genomic.fna/markers.fasta)
[2024-01-25 18:17:03,154] [INFO] Task started: Blastn
[2024-01-25 18:17:03,154] [INFO] Running command: blastn -query GCF_018271995.1_ASM1827199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f800763-135a-4230-8f81-fe310141c5ba/dqc_reference/reference_markers_gtdb.fasta -out GCF_018271995.1_ASM1827199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:17:03,945] [INFO] Task succeeded: Blastn
[2024-01-25 18:17:03,947] [INFO] Selected 16 target genomes.
[2024-01-25 18:17:03,947] [INFO] Target genome list was writen to GCF_018271995.1_ASM1827199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:17:03,957] [INFO] Task started: fastANI
[2024-01-25 18:17:03,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg038cb3c2-65c6-492e-a0e0-3924a4489962/GCF_018271995.1_ASM1827199v1_genomic.fna.gz --refList GCF_018271995.1_ASM1827199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018271995.1_ASM1827199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:17:19,045] [INFO] Task succeeded: fastANI
[2024-01-25 18:17:19,054] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:17:19,054] [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_018271995.1	s__Carboxylicivirga linearis	100.0	1950	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018156225.1	s__Carboxylicivirga sediminis	78.0135	228	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018271975.1	s__Carboxylicivirga mesophila	77.892	206	1953	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	77.6383	234	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016612505.1	s__Carboxylicivirga sp016612505	77.4614	239	1953	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	77.2935	174	1953	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	76.8975	114	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016342595.1	s__Carboxylicivirga sp016342595	76.7952	167	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Carboxylicivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003251015.1	s__SZUA-582 sp003251015	76.6718	76	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__SZUA-582	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005877885.1	s__Saccharicrinis sediminis	76.3772	123	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001660705.2	s__Saccharicrinis aurantiacus	76.3471	120	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Marinilabiliaceae;g__Saccharicrinis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010882175.1	s__Mangrovibacterium sp010882175	75.8387	53	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Mangrovibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005217565.1	s__Puteibacter caeruleilacunae	75.6614	59	1953	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Prolixibacteraceae;g__Puteibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:17:19,056] [INFO] GTDB search result was written to GCF_018271995.1_ASM1827199v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:17:19,056] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:17:19,059] [INFO] DFAST_QC result json was written to GCF_018271995.1_ASM1827199v1_genomic.fna/dqc_result.json
[2024-01-25 18:17:19,059] [INFO] DFAST_QC completed!
[2024-01-25 18:17:19,059] [INFO] Total running time: 0h1m43s