[2024-01-24 12:06:12,922] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:12,925] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:12,925] [INFO] DQC Reference Directory: /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference
[2024-01-24 12:06:14,295] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:14,296] [INFO] Task started: Prodigal
[2024-01-24 12:06:14,296] [INFO] Running command: gunzip -c /var/lib/cwl/stgd1ea55e5-bbfb-4906-95d1-229fa634b3c5/GCF_003676335.1_ASM367633v1_genomic.fna.gz | prodigal -d GCF_003676335.1_ASM367633v1_genomic.fna/cds.fna -a GCF_003676335.1_ASM367633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:23,897] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:23,898] [INFO] Task started: HMMsearch
[2024-01-24 12:06:23,898] [INFO] Running command: hmmsearch --tblout GCF_003676335.1_ASM367633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/reference_markers.hmm GCF_003676335.1_ASM367633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:24,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:24,259] [INFO] Found 6/6 markers.
[2024-01-24 12:06:24,307] [INFO] Query marker FASTA was written to GCF_003676335.1_ASM367633v1_genomic.fna/markers.fasta
[2024-01-24 12:06:24,308] [INFO] Task started: Blastn
[2024-01-24 12:06:24,308] [INFO] Running command: blastn -query GCF_003676335.1_ASM367633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/reference_markers.fasta -out GCF_003676335.1_ASM367633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:25,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:25,079] [INFO] Selected 15 target genomes.
[2024-01-24 12:06:25,080] [INFO] Target genome list was writen to GCF_003676335.1_ASM367633v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:25,092] [INFO] Task started: fastANI
[2024-01-24 12:06:25,092] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1ea55e5-bbfb-4906-95d1-229fa634b3c5/GCF_003676335.1_ASM367633v1_genomic.fna.gz --refList GCF_003676335.1_ASM367633v1_genomic.fna/target_genomes.txt --output GCF_003676335.1_ASM367633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:23,360] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:23,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:23,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:23,371] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:07:23,371] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:23,371] [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
Parashewanella spongiae	strain=KCTC 22492	GCA_003676335.1	342950	342950	type	True	100.0	1494	1506	95	conclusive
Parashewanella spongiae	strain=HJ039	GCA_004358345.1	342950	342950	type	True	99.9923	1504	1506	95	conclusive
Parashewanella spongiae	strain=KCTC 22492	GCA_023283745.1	342950	342950	type	True	99.9443	1411	1506	95	conclusive
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	78.4915	295	1506	95	below_threshold
Shewanella marina	strain=JCM 15074	GCA_000614975.1	487319	487319	type	True	78.1743	108	1506	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	78.099	104	1506	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	78.0177	124	1506	95	below_threshold
Parashewanella tropica	strain=MEBiC05444	GCA_004358445.1	2547970	2547970	type	True	77.9564	215	1506	95	below_threshold
Parashewanella curva	strain=C51	GCA_003675895.1	2338552	2338552	type	True	77.831	230	1506	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	77.6725	121	1506	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	77.6578	112	1506	95	below_threshold
Shewanella sairae	strain=LMG 21408	GCA_023283535.1	190310	190310	type	True	77.6442	124	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:23,373] [INFO] DFAST Taxonomy check result was written to GCF_003676335.1_ASM367633v1_genomic.fna/tc_result.tsv
[2024-01-24 12:07:23,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:23,374] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:23,374] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/checkm_data
[2024-01-24 12:07:23,375] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:23,428] [INFO] Task started: CheckM
[2024-01-24 12:07:23,428] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003676335.1_ASM367633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003676335.1_ASM367633v1_genomic.fna/checkm_input GCF_003676335.1_ASM367633v1_genomic.fna/checkm_result
[2024-01-24 12:07:56,787] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:56,788] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:56,810] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:56,810] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:56,810] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003676335.1_ASM367633v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:56,811] [INFO] Task started: Blastn
[2024-01-24 12:07:56,811] [INFO] Running command: blastn -query GCF_003676335.1_ASM367633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga69a6fb6-d757-4326-9845-ed9fefc21083/dqc_reference/reference_markers_gtdb.fasta -out GCF_003676335.1_ASM367633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:57,929] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:57,932] [INFO] Selected 18 target genomes.
[2024-01-24 12:07:57,932] [INFO] Target genome list was writen to GCF_003676335.1_ASM367633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:57,966] [INFO] Task started: fastANI
[2024-01-24 12:07:57,966] [INFO] Running command: fastANI --query /var/lib/cwl/stgd1ea55e5-bbfb-4906-95d1-229fa634b3c5/GCF_003676335.1_ASM367633v1_genomic.fna.gz --refList GCF_003676335.1_ASM367633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003676335.1_ASM367633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:30,832] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:30,848] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:30,848] [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_004358345.1	s__Parashewanella spongiae	99.9923	1504	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000013765.1	s__Shewanella denitrificans	78.5773	100	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900895.1	s__Parashewanella sp016900895	78.4776	295	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168585.1	s__Parashewanella sp004168585	78.2122	273	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000614975.1	s__Shewanella marina	78.1533	108	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019185.1	s__Shewanella halifaxensis	78.1377	109	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900456975.1	s__Shewanella baltica	78.136	124	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.88	96.32	0.89	0.85	16	-
GCF_003855395.1	s__Shewanella livingstonensis	78.0362	134	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000019525.1	s__Shewanella woodyi	78.0147	105	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_018221465.1	s__Shewanella intestini	77.9829	131	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004358445.1	s__Parashewanella tropica	77.9666	215	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	77.9128	132	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
GCF_011765625.1	s__Shewanella aestuarii_A	77.8792	138	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003797125.1	s__Shewanella frigidimarina	77.86	136	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.50	96.12	0.90	0.86	5	-
GCF_003675895.1	s__Parashewanella curva	77.8518	226	1506	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Parashewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:30,851] [INFO] GTDB search result was written to GCF_003676335.1_ASM367633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:30,852] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:30,855] [INFO] DFAST_QC result json was written to GCF_003676335.1_ASM367633v1_genomic.fna/dqc_result.json
[2024-01-24 12:08:30,855] [INFO] DFAST_QC completed!
[2024-01-24 12:08:30,856] [INFO] Total running time: 0h2m18s