[2024-01-24 10:58:06,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference
[2024-01-24 10:58:09,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,643] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,643] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d8876f8-006a-4093-962e-523bbecb8444/GCF_014651955.1_ASM1465195v1_genomic.fna.gz | prodigal -d GCF_014651955.1_ASM1465195v1_genomic.fna/cds.fna -a GCF_014651955.1_ASM1465195v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:20,233] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:20,234] [INFO] Task started: HMMsearch
[2024-01-24 10:58:20,234] [INFO] Running command: hmmsearch --tblout GCF_014651955.1_ASM1465195v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/reference_markers.hmm GCF_014651955.1_ASM1465195v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:20,598] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:20,599] [INFO] Found 6/6 markers.
[2024-01-24 10:58:20,638] [INFO] Query marker FASTA was written to GCF_014651955.1_ASM1465195v1_genomic.fna/markers.fasta
[2024-01-24 10:58:20,639] [INFO] Task started: Blastn
[2024-01-24 10:58:20,639] [INFO] Running command: blastn -query GCF_014651955.1_ASM1465195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/reference_markers.fasta -out GCF_014651955.1_ASM1465195v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:21,355] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:21,358] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:21,358] [INFO] Target genome list was writen to GCF_014651955.1_ASM1465195v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:21,368] [INFO] Task started: fastANI
[2024-01-24 10:58:21,368] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8876f8-006a-4093-962e-523bbecb8444/GCF_014651955.1_ASM1465195v1_genomic.fna.gz --refList GCF_014651955.1_ASM1465195v1_genomic.fna/target_genomes.txt --output GCF_014651955.1_ASM1465195v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:32,453] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:32,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:32,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:32,471] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:32,472] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:32,472] [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
Shewanella fodinae	strain=KCTC 22506	GCA_014651955.1	552357	552357	type	True	100.0	1275	1278	95	conclusive
Shewanella fodinae	strain=CCUG 57102	GCA_023349145.1	552357	552357	type	True	99.9924	1259	1278	95	conclusive
Shewanella dokdonensis	strain=DSM 23626	GCA_018394335.1	712036	712036	type	True	85.6192	1064	1278	95	below_threshold
Shewanella yunxiaonensis	strain=FJAT-54481	GCA_018223345.1	2829809	2829809	type	True	81.3347	719	1278	95	below_threshold
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	78.1854	229	1278	95	below_threshold
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	78.1708	227	1278	95	below_threshold
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	78.1342	289	1278	95	below_threshold
Shewanella sedimentimangrovi	strain=FJAT-52962	GCA_017354965.1	2814293	2814293	type	True	77.9721	169	1278	95	below_threshold
Shewanella oneidensis	strain=MR-1	GCA_013267215.1	70863	70863	type	True	77.9429	161	1278	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	77.2988	80	1278	95	below_threshold
Shewanella canadensis	strain=HAW-EB2	GCA_003966225.1	271096	271096	type	True	77.0312	101	1278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:32,473] [INFO] DFAST Taxonomy check result was written to GCF_014651955.1_ASM1465195v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:32,474] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:32,474] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:32,474] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/checkm_data
[2024-01-24 10:58:32,476] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:32,523] [INFO] Task started: CheckM
[2024-01-24 10:58:32,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014651955.1_ASM1465195v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014651955.1_ASM1465195v1_genomic.fna/checkm_input GCF_014651955.1_ASM1465195v1_genomic.fna/checkm_result
[2024-01-24 10:59:08,739] [INFO] Task succeeded: CheckM
[2024-01-24 10:59:08,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,760] [INFO] ===== Completeness check finished =====
[2024-01-24 10:59:08,760] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:59:08,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014651955.1_ASM1465195v1_genomic.fna/markers.fasta)
[2024-01-24 10:59:08,761] [INFO] Task started: Blastn
[2024-01-24 10:59:08,761] [INFO] Running command: blastn -query GCF_014651955.1_ASM1465195v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg926faf34-d091-46a2-978d-f9a01ec26364/dqc_reference/reference_markers_gtdb.fasta -out GCF_014651955.1_ASM1465195v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:59:09,890] [INFO] Task succeeded: Blastn
[2024-01-24 10:59:09,893] [INFO] Selected 16 target genomes.
[2024-01-24 10:59:09,894] [INFO] Target genome list was writen to GCF_014651955.1_ASM1465195v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:59:09,920] [INFO] Task started: fastANI
[2024-01-24 10:59:09,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8876f8-006a-4093-962e-523bbecb8444/GCF_014651955.1_ASM1465195v1_genomic.fna.gz --refList GCF_014651955.1_ASM1465195v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014651955.1_ASM1465195v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:22,500] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:22,519] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:22,519] [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_014651955.1	s__Shewanella fodinae	100.0	1275	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.57	97.13	0.90	0.90	3	conclusive
GCF_018394335.1	s__Shewanella dokdonensis	85.6151	1064	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018223345.1	s__Shewanella sp018223345	81.3437	717	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000753795.1	s__Shewanella mangrovi	78.1817	291	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017354945.1	s__Shewanella sp017354945	78.1314	288	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000015245.1	s__Shewanella amazonensis	78.1288	158	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000146165.2	s__Shewanella oneidensis	77.9988	164	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_002836945.1	s__Shewanella chilikensis	77.9652	225	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	99.40	98.79	0.97	0.93	5	-
GCF_017354985.1	s__Shewanella sp017354985	77.9256	164	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_014647855.1	s__Shewanella gelidii	77.8535	77	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016406305.1	s__Shewanella putrefaciens_C	77.6814	168	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002215585.1	s__Shewanella marisflavi	77.5731	123	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.20	98.16	0.93	0.93	3	-
GCF_000518705.1	s__Shewanella colwelliana	77.4754	97	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_003966225.1	s__Shewanella canadensis	77.0297	101	1278	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:22,521] [INFO] GTDB search result was written to GCF_014651955.1_ASM1465195v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:22,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:22,535] [INFO] DFAST_QC result json was written to GCF_014651955.1_ASM1465195v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:22,536] [INFO] DFAST_QC completed!
[2024-01-24 10:59:22,536] [INFO] Total running time: 0h1m16s