[2024-01-24 12:06:24,645] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference
[2024-01-24 12:06:26,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:26,029] [INFO] Task started: Prodigal
[2024-01-24 12:06:26,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg9fc91076-728a-4f3f-aa49-ed7f2d0bdc5c/GCF_002000025.1_ASM200002v1_genomic.fna.gz | prodigal -d GCF_002000025.1_ASM200002v1_genomic.fna/cds.fna -a GCF_002000025.1_ASM200002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:34,617] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:34,618] [INFO] Task started: HMMsearch
[2024-01-24 12:06:34,618] [INFO] Running command: hmmsearch --tblout GCF_002000025.1_ASM200002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/reference_markers.hmm GCF_002000025.1_ASM200002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:34,933] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:34,935] [INFO] Found 6/6 markers.
[2024-01-24 12:06:34,971] [INFO] Query marker FASTA was written to GCF_002000025.1_ASM200002v1_genomic.fna/markers.fasta
[2024-01-24 12:06:34,971] [INFO] Task started: Blastn
[2024-01-24 12:06:34,972] [INFO] Running command: blastn -query GCF_002000025.1_ASM200002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/reference_markers.fasta -out GCF_002000025.1_ASM200002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:35,706] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:35,711] [INFO] Selected 19 target genomes.
[2024-01-24 12:06:35,711] [INFO] Target genome list was writen to GCF_002000025.1_ASM200002v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:35,719] [INFO] Task started: fastANI
[2024-01-24 12:06:35,719] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc91076-728a-4f3f-aa49-ed7f2d0bdc5c/GCF_002000025.1_ASM200002v1_genomic.fna.gz --refList GCF_002000025.1_ASM200002v1_genomic.fna/target_genomes.txt --output GCF_002000025.1_ASM200002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:49,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:49,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:49,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:49,718] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:06:49,719] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:06:49,719] [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
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	80.2669	648	1415	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_002104455.1	641665	641665	type	True	79.5879	502	1415	95	below_threshold
Colwellia chukchiensis	strain=CGMCC 1.9127	GCA_900109795.1	641665	641665	type	True	79.5632	506	1415	95	below_threshold
Pseudocolwellia agarivorans	strain=QM50	GCA_002000085.1	1911682	1911682	type	True	78.4685	258	1415	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.3265	225	1415	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	78.198	242	1415	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.0468	319	1415	95	below_threshold
Thalassotalea profundi	strain=CGMCC 1.15922	GCA_014653195.1	2036687	2036687	type	True	78.0404	255	1415	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	78.0104	279	1415	95	below_threshold
Litorilituus sediminis	strain=JCM 17549	GCA_004295665.1	718192	718192	type	True	78.0005	254	1415	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	77.7528	264	1415	95	below_threshold
Thalassotalea marina	strain=KCTC 42731	GCA_014656435.1	1673741	1673741	type	True	77.6048	189	1415	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:49,721] [INFO] DFAST Taxonomy check result was written to GCF_002000025.1_ASM200002v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:49,722] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:49,722] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:49,722] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/checkm_data
[2024-01-24 12:06:49,724] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:49,771] [INFO] Task started: CheckM
[2024-01-24 12:06:49,772] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002000025.1_ASM200002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002000025.1_ASM200002v1_genomic.fna/checkm_input GCF_002000025.1_ASM200002v1_genomic.fna/checkm_result
[2024-01-24 12:07:19,130] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:19,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:19,154] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:19,154] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:19,155] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002000025.1_ASM200002v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:19,155] [INFO] Task started: Blastn
[2024-01-24 12:07:19,155] [INFO] Running command: blastn -query GCF_002000025.1_ASM200002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg44357bd1-8d96-4062-ac98-3eb8a58f67be/dqc_reference/reference_markers_gtdb.fasta -out GCF_002000025.1_ASM200002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:20,251] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:20,255] [INFO] Selected 12 target genomes.
[2024-01-24 12:07:20,255] [INFO] Target genome list was writen to GCF_002000025.1_ASM200002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:20,265] [INFO] Task started: fastANI
[2024-01-24 12:07:20,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg9fc91076-728a-4f3f-aa49-ed7f2d0bdc5c/GCF_002000025.1_ASM200002v1_genomic.fna.gz --refList GCF_002000025.1_ASM200002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002000025.1_ASM200002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:31,466] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:31,477] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:31,477] [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_002000025.1	s__Cognaticolwellia aestuarii	100.0	1411	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_003354085.1	s__Cognaticolwellia sp003354085	82.0498	860	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003971255.1	s__Cognaticolwellia sp003971255	81.7219	889	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104515.1	s__Cognaticolwellia polaris	80.884	691	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077505.1	s__Cognaticolwellia sp014077505	80.692	692	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002076895.1	s__Cognaticolwellia beringensis	80.6629	704	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002104535.1	s__Cognaticolwellia sediminilitoris	80.5199	648	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077175.1	s__Cognaticolwellia sp002077175	80.4713	688	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003061515.1	s__Cognaticolwellia sp003061515	80.4426	662	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.05	98.05	0.90	0.90	2	-
GCF_007954265.1	s__Cognaticolwellia sp007954265	80.3717	646	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014077005.1	s__Cognaticolwellia sp014077005	80.2707	656	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	98.22	95.22	0.95	0.87	11	-
GCF_014077095.1	s__Cognaticolwellia sp014077095	80.1018	640	1415	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Cognaticolwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:31,480] [INFO] GTDB search result was written to GCF_002000025.1_ASM200002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:31,480] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:31,484] [INFO] DFAST_QC result json was written to GCF_002000025.1_ASM200002v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:31,485] [INFO] DFAST_QC completed!
[2024-01-24 12:07:31,485] [INFO] Total running time: 0h1m7s