[2024-01-24 11:51:08,508] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:08,510] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:08,510] [INFO] DQC Reference Directory: /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference
[2024-01-24 11:51:09,708] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:09,709] [INFO] Task started: Prodigal
[2024-01-24 11:51:09,710] [INFO] Running command: gunzip -c /var/lib/cwl/stg8261ac87-922b-4a57-90f8-2c717c1d03f7/GCF_019457655.1_ASM1945765v1_genomic.fna.gz | prodigal -d GCF_019457655.1_ASM1945765v1_genomic.fna/cds.fna -a GCF_019457655.1_ASM1945765v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:21,863] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:21,863] [INFO] Task started: HMMsearch
[2024-01-24 11:51:21,864] [INFO] Running command: hmmsearch --tblout GCF_019457655.1_ASM1945765v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/reference_markers.hmm GCF_019457655.1_ASM1945765v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:22,172] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:22,173] [INFO] Found 6/6 markers.
[2024-01-24 11:51:22,214] [INFO] Query marker FASTA was written to GCF_019457655.1_ASM1945765v1_genomic.fna/markers.fasta
[2024-01-24 11:51:22,215] [INFO] Task started: Blastn
[2024-01-24 11:51:22,215] [INFO] Running command: blastn -query GCF_019457655.1_ASM1945765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/reference_markers.fasta -out GCF_019457655.1_ASM1945765v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:23,062] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:23,068] [INFO] Selected 12 target genomes.
[2024-01-24 11:51:23,069] [INFO] Target genome list was writen to GCF_019457655.1_ASM1945765v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:23,073] [INFO] Task started: fastANI
[2024-01-24 11:51:23,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg8261ac87-922b-4a57-90f8-2c717c1d03f7/GCF_019457655.1_ASM1945765v1_genomic.fna.gz --refList GCF_019457655.1_ASM1945765v1_genomic.fna/target_genomes.txt --output GCF_019457655.1_ASM1945765v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:34,317] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:34,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:34,318] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:34,328] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:34,328] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:34,328] [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 loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	96.1419	1448	1526	95	conclusive
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	90.6693	1372	1526	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	90.5274	1347	1526	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	84.6884	1186	1526	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	79.8838	351	1526	95	below_threshold
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	79.7856	532	1526	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	79.4451	489	1526	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	78.4316	409	1526	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.3418	444	1526	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	78.1526	272	1526	95	below_threshold
Shewanella carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	78.0376	421	1526	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	77.9171	423	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:34,330] [INFO] DFAST Taxonomy check result was written to GCF_019457655.1_ASM1945765v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:34,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:34,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:34,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/checkm_data
[2024-01-24 11:51:34,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:34,385] [INFO] Task started: CheckM
[2024-01-24 11:51:34,386] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019457655.1_ASM1945765v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019457655.1_ASM1945765v1_genomic.fna/checkm_input GCF_019457655.1_ASM1945765v1_genomic.fna/checkm_result
[2024-01-24 11:52:11,952] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:11,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.88%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:11,975] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:11,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:11,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019457655.1_ASM1945765v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:11,976] [INFO] Task started: Blastn
[2024-01-24 11:52:11,976] [INFO] Running command: blastn -query GCF_019457655.1_ASM1945765v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgee1f1d44-e471-47a5-864c-8bcd803d8244/dqc_reference/reference_markers_gtdb.fasta -out GCF_019457655.1_ASM1945765v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:13,200] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:13,203] [INFO] Selected 9 target genomes.
[2024-01-24 11:52:13,203] [INFO] Target genome list was writen to GCF_019457655.1_ASM1945765v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:13,209] [INFO] Task started: fastANI
[2024-01-24 11:52:13,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg8261ac87-922b-4a57-90f8-2c717c1d03f7/GCF_019457655.1_ASM1945765v1_genomic.fna.gz --refList GCF_019457655.1_ASM1945765v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019457655.1_ASM1945765v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:22,113] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:22,121] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:22,121] [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_000016065.1	s__Shewanella loihica	96.1533	1447	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	conclusive
GCF_009831655.1	s__Shewanella insulae	90.6693	1372	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000832025.1	s__Shewanella sp000832025	89.0399	1322	1526	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	84.7752	1199	1526	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	79.7922	532	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.91	98.91	0.92	0.92	2	-
GCF_003605125.1	s__Shewanella algidipiscicola	79.4568	487	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_017354985.1	s__Shewanella sp017354985	78.3911	408	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_012911865.1	s__Shewanella sp012911865	78.3422	444	1526	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003353085.1	s__Shewanella corallii	78.2496	271	1526	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 11:52:22,123] [INFO] GTDB search result was written to GCF_019457655.1_ASM1945765v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:22,123] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:22,126] [INFO] DFAST_QC result json was written to GCF_019457655.1_ASM1945765v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:22,127] [INFO] DFAST_QC completed!
[2024-01-24 11:52:22,127] [INFO] Total running time: 0h1m14s