[2024-01-25 20:13:50,684] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,686] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,686] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference
[2024-01-25 20:13:51,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,796] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgabd680c9-8812-4207-8b68-532c7b0aaba2/GCF_009831655.1_ASM983165v1_genomic.fna.gz | prodigal -d GCF_009831655.1_ASM983165v1_genomic.fna/cds.fna -a GCF_009831655.1_ASM983165v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:02,324] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:02,324] [INFO] Task started: HMMsearch
[2024-01-25 20:14:02,324] [INFO] Running command: hmmsearch --tblout GCF_009831655.1_ASM983165v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/reference_markers.hmm GCF_009831655.1_ASM983165v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:02,627] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:02,630] [INFO] Found 6/6 markers.
[2024-01-25 20:14:02,670] [INFO] Query marker FASTA was written to GCF_009831655.1_ASM983165v1_genomic.fna/markers.fasta
[2024-01-25 20:14:02,670] [INFO] Task started: Blastn
[2024-01-25 20:14:02,670] [INFO] Running command: blastn -query GCF_009831655.1_ASM983165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/reference_markers.fasta -out GCF_009831655.1_ASM983165v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:03,479] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:03,493] [INFO] Selected 10 target genomes.
[2024-01-25 20:14:03,494] [INFO] Target genome list was writen to GCF_009831655.1_ASM983165v1_genomic.fna/target_genomes.txt
[2024-01-25 20:14:03,498] [INFO] Task started: fastANI
[2024-01-25 20:14:03,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd680c9-8812-4207-8b68-532c7b0aaba2/GCF_009831655.1_ASM983165v1_genomic.fna.gz --refList GCF_009831655.1_ASM983165v1_genomic.fna/target_genomes.txt --output GCF_009831655.1_ASM983165v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:14,065] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:14,065] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:14,065] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:14,073] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:14:14,073] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:14,073] [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 insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	100.0	1529	1533	95	conclusive
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	90.6663	1374	1533	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	90.0368	1343	1533	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	84.3938	1178	1533	95	below_threshold
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	79.6758	536	1533	95	below_threshold
Shewanella seohaensis	strain=KCTC 23556	GCA_025449215.1	755175	755175	type	True	79.3834	341	1533	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.0896	432	1533	95	below_threshold
Shewanella sedimentimangrovi	strain=FJAT-52962	GCA_017354965.1	2814293	2814293	type	True	77.9628	367	1533	95	below_threshold
Shewanella corallii	strain=DSM 21332	GCA_023349125.1	560080	560080	type	True	77.9458	261	1533	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	77.9389	361	1533	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:14,074] [INFO] DFAST Taxonomy check result was written to GCF_009831655.1_ASM983165v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:14,075] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:14,075] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:14,076] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/checkm_data
[2024-01-25 20:14:14,076] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:14,122] [INFO] Task started: CheckM
[2024-01-25 20:14:14,122] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009831655.1_ASM983165v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009831655.1_ASM983165v1_genomic.fna/checkm_input GCF_009831655.1_ASM983165v1_genomic.fna/checkm_result
[2024-01-25 20:14:47,096] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:47,097] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:47,114] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:47,114] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:47,115] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009831655.1_ASM983165v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:47,115] [INFO] Task started: Blastn
[2024-01-25 20:14:47,115] [INFO] Running command: blastn -query GCF_009831655.1_ASM983165v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc6b9515-3aca-4679-b506-057d311f1f50/dqc_reference/reference_markers_gtdb.fasta -out GCF_009831655.1_ASM983165v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:48,340] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:48,343] [INFO] Selected 7 target genomes.
[2024-01-25 20:14:48,343] [INFO] Target genome list was writen to GCF_009831655.1_ASM983165v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:48,349] [INFO] Task started: fastANI
[2024-01-25 20:14:48,349] [INFO] Running command: fastANI --query /var/lib/cwl/stgabd680c9-8812-4207-8b68-532c7b0aaba2/GCF_009831655.1_ASM983165v1_genomic.fna.gz --refList GCF_009831655.1_ASM983165v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009831655.1_ASM983165v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:56,017] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:56,023] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:56,023] [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_009831655.1	s__Shewanella insulae	100.0	1529	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000016065.1	s__Shewanella loihica	90.6714	1373	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_000832025.1	s__Shewanella sp000832025	89.1824	1326	1533	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	84.3704	1145	1533	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	79.6923	536	1533	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	79.5737	488	1533	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	77.9395	361	1533	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:56,025] [INFO] GTDB search result was written to GCF_009831655.1_ASM983165v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:56,025] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:56,028] [INFO] DFAST_QC result json was written to GCF_009831655.1_ASM983165v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:56,028] [INFO] DFAST_QC completed!
[2024-01-25 20:14:56,028] [INFO] Total running time: 0h1m5s