[2024-01-24 12:37:24,869] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,875] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,875] [INFO] DQC Reference Directory: /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference
[2024-01-24 12:37:26,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,196] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,196] [INFO] Running command: gunzip -c /var/lib/cwl/stg27c8805a-d2e2-4f61-a5e8-8ee5936959d9/GCF_021389935.1_ASM2138993v1_genomic.fna.gz | prodigal -d GCF_021389935.1_ASM2138993v1_genomic.fna/cds.fna -a GCF_021389935.1_ASM2138993v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:50,496] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:50,496] [INFO] Task started: HMMsearch
[2024-01-24 12:37:50,496] [INFO] Running command: hmmsearch --tblout GCF_021389935.1_ASM2138993v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/reference_markers.hmm GCF_021389935.1_ASM2138993v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:50,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:50,808] [INFO] Found 6/6 markers.
[2024-01-24 12:37:50,859] [INFO] Query marker FASTA was written to GCF_021389935.1_ASM2138993v1_genomic.fna/markers.fasta
[2024-01-24 12:37:50,859] [INFO] Task started: Blastn
[2024-01-24 12:37:50,860] [INFO] Running command: blastn -query GCF_021389935.1_ASM2138993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/reference_markers.fasta -out GCF_021389935.1_ASM2138993v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:51,469] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:51,471] [INFO] Selected 20 target genomes.
[2024-01-24 12:37:51,472] [INFO] Target genome list was writen to GCF_021389935.1_ASM2138993v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:51,484] [INFO] Task started: fastANI
[2024-01-24 12:37:51,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c8805a-d2e2-4f61-a5e8-8ee5936959d9/GCF_021389935.1_ASM2138993v1_genomic.fna.gz --refList GCF_021389935.1_ASM2138993v1_genomic.fna/target_genomes.txt --output GCF_021389935.1_ASM2138993v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:38:06,149] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:06,150] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:38:06,150] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:38:06,159] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:38:06,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:38:06,159] [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
Fulvivirga sediminis	strain=2943	GCA_016757215.1	2803949	2803949	type	True	78.6726	476	2174	95	below_threshold
Fulvivirga lutea	strain=S481	GCA_017068455.1	2810512	2810512	type	True	77.335	91	2174	95	below_threshold
Fulvivirga marina	strain=29W222	GCA_016775155.1	2494733	2494733	type	True	77.0138	154	2174	95	below_threshold
Fulvivirga lutimaris	strain=KCTC 42720	GCA_009711525.1	1819566	1819566	type	True	76.9881	112	2174	95	below_threshold
Fulvivirga imtechensis	strain=AK7	GCA_000331535.1	881893	881893	type	True	76.9603	126	2174	95	below_threshold
Fulvivirga kasyanovii	strain=JCM 16186	GCA_009711405.1	396812	396812	type	True	76.9505	135	2174	95	below_threshold
Fulvivirga aurantia	strain=RKSG066	GCA_009711475.1	2529383	2529383	type	True	76.6625	99	2174	95	below_threshold
Marivirga atlantica	strain=SM1354	GCA_016734805.1	1548457	1548457	type	True	75.7236	56	2174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:38:06,161] [INFO] DFAST Taxonomy check result was written to GCF_021389935.1_ASM2138993v1_genomic.fna/tc_result.tsv
[2024-01-24 12:38:06,161] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:38:06,161] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:38:06,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/checkm_data
[2024-01-24 12:38:06,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:38:06,221] [INFO] Task started: CheckM
[2024-01-24 12:38:06,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021389935.1_ASM2138993v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021389935.1_ASM2138993v1_genomic.fna/checkm_input GCF_021389935.1_ASM2138993v1_genomic.fna/checkm_result
[2024-01-24 12:39:15,024] [INFO] Task succeeded: CheckM
[2024-01-24 12:39:15,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:39:15,049] [INFO] ===== Completeness check finished =====
[2024-01-24 12:39:15,050] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:39:15,050] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021389935.1_ASM2138993v1_genomic.fna/markers.fasta)
[2024-01-24 12:39:15,050] [INFO] Task started: Blastn
[2024-01-24 12:39:15,051] [INFO] Running command: blastn -query GCF_021389935.1_ASM2138993v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16d42246-8210-48bf-88ea-6852d7a4b707/dqc_reference/reference_markers_gtdb.fasta -out GCF_021389935.1_ASM2138993v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:15,820] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:15,825] [INFO] Selected 19 target genomes.
[2024-01-24 12:39:15,825] [INFO] Target genome list was writen to GCF_021389935.1_ASM2138993v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:39:15,870] [INFO] Task started: fastANI
[2024-01-24 12:39:15,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c8805a-d2e2-4f61-a5e8-8ee5936959d9/GCF_021389935.1_ASM2138993v1_genomic.fna.gz --refList GCF_021389935.1_ASM2138993v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021389935.1_ASM2138993v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:39:29,251] [INFO] Task succeeded: fastANI
[2024-01-24 12:39:29,262] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:39:29,263] [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_016757215.1	s__Fulvivirga sp016757215	78.6729	475	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017068455.1	s__Fulvivirga sp017068455	77.342	91	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016775155.1	s__Fulvivirga sp016775155	77.0279	153	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711525.1	s__Fulvivirga lutimaris	76.9881	112	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711405.1	s__Fulvivirga kasyanovii	76.9647	135	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000331535.1	s__Fulvivirga imtechensis	76.9603	126	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711475.1	s__Fulvivirga aurantia	76.6625	99	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Fulvivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016734805.1	s__Marivirga atlantica	75.7236	56	2174	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Marivirga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:39:29,264] [INFO] GTDB search result was written to GCF_021389935.1_ASM2138993v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:39:29,265] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:39:29,268] [INFO] DFAST_QC result json was written to GCF_021389935.1_ASM2138993v1_genomic.fna/dqc_result.json
[2024-01-24 12:39:29,268] [INFO] DFAST_QC completed!
[2024-01-24 12:39:29,268] [INFO] Total running time: 0h2m4s