[2024-01-24 11:51:11,386] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,388] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,388] [INFO] DQC Reference Directory: /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference
[2024-01-24 11:51:12,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,913] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,913] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf44e0b5-b6fa-4a28-b1c0-b1a9d9b6c534/GCF_007004545.3_ASM700454v3_genomic.fna.gz | prodigal -d GCF_007004545.3_ASM700454v3_genomic.fna/cds.fna -a GCF_007004545.3_ASM700454v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:26,060] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:26,060] [INFO] Task started: HMMsearch
[2024-01-24 11:51:26,060] [INFO] Running command: hmmsearch --tblout GCF_007004545.3_ASM700454v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/reference_markers.hmm GCF_007004545.3_ASM700454v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:26,439] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:26,441] [INFO] Found 6/6 markers.
[2024-01-24 11:51:26,488] [INFO] Query marker FASTA was written to GCF_007004545.3_ASM700454v3_genomic.fna/markers.fasta
[2024-01-24 11:51:26,488] [INFO] Task started: Blastn
[2024-01-24 11:51:26,488] [INFO] Running command: blastn -query GCF_007004545.3_ASM700454v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/reference_markers.fasta -out GCF_007004545.3_ASM700454v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:27,199] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:27,203] [INFO] Selected 13 target genomes.
[2024-01-24 11:51:27,204] [INFO] Target genome list was writen to GCF_007004545.3_ASM700454v3_genomic.fna/target_genomes.txt
[2024-01-24 11:51:27,249] [INFO] Task started: fastANI
[2024-01-24 11:51:27,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf44e0b5-b6fa-4a28-b1c0-b1a9d9b6c534/GCF_007004545.3_ASM700454v3_genomic.fna.gz --refList GCF_007004545.3_ASM700454v3_genomic.fna/target_genomes.txt --output GCF_007004545.3_ASM700454v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:43,018] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:43,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:43,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:43,030] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:43,030] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:43,031] [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 eurypsychrophilus	strain=YLB-08	GCA_007004545.3	2593656	2593656	type	True	100.0	1947	1950	95	conclusive
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	82.8594	1099	1950	95	below_threshold
Shewanella benthica	strain=DSM 8812	GCA_015069875.1	43661	43661	type	True	82.6055	810	1950	95	below_threshold
Shewanella psychropiezotolerans	strain=YLB-06	GCA_007197555.1	2593655	2593655	type	True	82.3326	1121	1950	95	below_threshold
Shewanella violacea	strain=DSS12	GCA_000091325.1	60217	60217	type	True	81.3129	866	1950	95	below_threshold
Shewanella canadensis	strain=HAW-EB2	GCA_003966225.1	271096	271096	type	True	80.3943	674	1950	95	below_threshold
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	80.0148	635	1950	95	below_threshold
Shewanella abyssi	strain=DSM 17171	GCA_023284025.1	311789	311789	type	True	79.411	392	1950	95	below_threshold
Shewanella gelidimarina	strain=ATCC 700752	GCA_023283945.1	56813	56813	type	True	79.0918	396	1950	95	below_threshold
Shewanella kaireitica	strain=DSM 17170	GCA_023284045.1	212021	212021	type	True	78.6002	396	1950	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	77.8569	182	1950	95	below_threshold
Shewanella basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	77.6588	177	1950	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.5912	142	1950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:43,033] [INFO] DFAST Taxonomy check result was written to GCF_007004545.3_ASM700454v3_genomic.fna/tc_result.tsv
[2024-01-24 11:51:43,033] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:43,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:43,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/checkm_data
[2024-01-24 11:51:43,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:43,128] [INFO] Task started: CheckM
[2024-01-24 11:51:43,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007004545.3_ASM700454v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007004545.3_ASM700454v3_genomic.fna/checkm_input GCF_007004545.3_ASM700454v3_genomic.fna/checkm_result
[2024-01-24 11:52:24,162] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:24,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,181] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:24,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:24,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007004545.3_ASM700454v3_genomic.fna/markers.fasta)
[2024-01-24 11:52:24,182] [INFO] Task started: Blastn
[2024-01-24 11:52:24,182] [INFO] Running command: blastn -query GCF_007004545.3_ASM700454v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg00f6f225-c1ad-473d-bbfd-6af19fb0dc8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007004545.3_ASM700454v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:25,052] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:25,055] [INFO] Selected 13 target genomes.
[2024-01-24 11:52:25,055] [INFO] Target genome list was writen to GCF_007004545.3_ASM700454v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:25,064] [INFO] Task started: fastANI
[2024-01-24 11:52:25,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf44e0b5-b6fa-4a28-b1c0-b1a9d9b6c534/GCF_007004545.3_ASM700454v3_genomic.fna.gz --refList GCF_007004545.3_ASM700454v3_genomic.fna/target_genomes_gtdb.txt --output GCF_007004545.3_ASM700454v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:41,849] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:41,860] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:41,861] [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_007004545.2	s__Shewanella sp007004545	99.9546	1911	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCF_002005305.1	s__Shewanella psychrophila	82.8534	1099	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015069875.1	s__Shewanella benthica	82.5876	814	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.81	96.81	0.66	0.66	2	-
GCF_007197555.1	s__Shewanella sp007197555	82.3432	1118	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.43	99.43	0.94	0.94	2	-
GCF_000172075.1	s__Shewanella benthica_A	81.5466	856	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.25	96.25	0.86	0.86	2	-
GCF_000091325.1	s__Shewanella violacea	81.3252	867	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001957125.1	s__Shewanella sp001957125	81.2509	1070	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214165.1	s__Shewanella sp013214165	81.1366	784	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966225.1	s__Shewanella canadensis	80.4047	670	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966265.1	s__Shewanella atlantica	80.0082	632	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014885.1	s__Shewanella piezotolerans	79.6148	386	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018285.1	s__Shewanella pealeana	79.3809	420	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003605125.1	s__Shewanella algidipiscicola	78.5543	334	1950	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:41,863] [INFO] GTDB search result was written to GCF_007004545.3_ASM700454v3_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:41,863] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:41,866] [INFO] DFAST_QC result json was written to GCF_007004545.3_ASM700454v3_genomic.fna/dqc_result.json
[2024-01-24 11:52:41,867] [INFO] DFAST_QC completed!
[2024-01-24 11:52:41,867] [INFO] Total running time: 0h1m30s