[2024-01-24 12:15:18,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference
[2024-01-24 12:15:19,763] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:19,764] [INFO] Task started: Prodigal
[2024-01-24 12:15:19,764] [INFO] Running command: gunzip -c /var/lib/cwl/stgb055ceb7-2799-43a7-b53e-8dd86d3a2541/GCF_005885605.1_ASM588560v1_genomic.fna.gz | prodigal -d GCF_005885605.1_ASM588560v1_genomic.fna/cds.fna -a GCF_005885605.1_ASM588560v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:26,907] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:26,907] [INFO] Task started: HMMsearch
[2024-01-24 12:15:26,907] [INFO] Running command: hmmsearch --tblout GCF_005885605.1_ASM588560v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/reference_markers.hmm GCF_005885605.1_ASM588560v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:27,156] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:27,159] [INFO] Found 6/6 markers.
[2024-01-24 12:15:27,191] [INFO] Query marker FASTA was written to GCF_005885605.1_ASM588560v1_genomic.fna/markers.fasta
[2024-01-24 12:15:27,192] [INFO] Task started: Blastn
[2024-01-24 12:15:27,192] [INFO] Running command: blastn -query GCF_005885605.1_ASM588560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/reference_markers.fasta -out GCF_005885605.1_ASM588560v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:27,947] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:27,951] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:27,952] [INFO] Target genome list was writen to GCF_005885605.1_ASM588560v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:27,957] [INFO] Task started: fastANI
[2024-01-24 12:15:27,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgb055ceb7-2799-43a7-b53e-8dd86d3a2541/GCF_005885605.1_ASM588560v1_genomic.fna.gz --refList GCF_005885605.1_ASM588560v1_genomic.fna/target_genomes.txt --output GCF_005885605.1_ASM588560v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:36,852] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:36,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:36,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:36,863] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:36,863] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:36,864] [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
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	100.0	1191	1191	95	conclusive
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	80.8981	698	1191	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	79.9799	553	1191	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	79.9418	459	1191	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	79.6818	574	1191	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	78.3026	254	1191	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	76.735	87	1191	95	below_threshold
Shewanella vesiculosa	strain=M7	GCA_021560015.1	518738	518738	type	True	76.3085	67	1191	95	below_threshold
Aliivibrio fischeri	strain=DSM 507	GCA_023983475.1	668	668	suspected-type	True	76.2675	58	1191	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	75.8718	67	1191	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:36,870] [INFO] DFAST Taxonomy check result was written to GCF_005885605.1_ASM588560v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:36,873] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:36,873] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:36,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/checkm_data
[2024-01-24 12:15:36,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:36,915] [INFO] Task started: CheckM
[2024-01-24 12:15:36,915] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005885605.1_ASM588560v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005885605.1_ASM588560v1_genomic.fna/checkm_input GCF_005885605.1_ASM588560v1_genomic.fna/checkm_result
[2024-01-24 12:16:01,707] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:01,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:01,731] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:01,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:01,732] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005885605.1_ASM588560v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:01,732] [INFO] Task started: Blastn
[2024-01-24 12:16:01,732] [INFO] Running command: blastn -query GCF_005885605.1_ASM588560v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb4f550c-9f37-4291-a3d9-980a7b1c5e4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_005885605.1_ASM588560v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:02,812] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:02,815] [INFO] Selected 9 target genomes.
[2024-01-24 12:16:02,815] [INFO] Target genome list was writen to GCF_005885605.1_ASM588560v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:02,821] [INFO] Task started: fastANI
[2024-01-24 12:16:02,821] [INFO] Running command: fastANI --query /var/lib/cwl/stgb055ceb7-2799-43a7-b53e-8dd86d3a2541/GCF_005885605.1_ASM588560v1_genomic.fna.gz --refList GCF_005885605.1_ASM588560v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005885605.1_ASM588560v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:11,269] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,277] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:11,277] [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_005885605.1	s__Colwellia ponticola	100.0	1191	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002836775.1	s__Colwellia sp002836775	81.1579	687	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	80.9786	689	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	80.8965	698	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	80.8176	623	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	80.8168	696	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_003545415.1	s__Colwellia sp003545415	80.7615	532	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214175.1	s__Colwellia sp013214175	80.3414	603	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	-
GCF_002843355.2	s__Colwellia echini	79.96	457	1191	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,280] [INFO] GTDB search result was written to GCF_005885605.1_ASM588560v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:11,280] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:11,284] [INFO] DFAST_QC result json was written to GCF_005885605.1_ASM588560v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:11,284] [INFO] DFAST_QC completed!
[2024-01-24 12:16:11,284] [INFO] Total running time: 0h0m53s