[2024-01-24 11:36:20,682] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:36:20,685] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:36:20,685] [INFO] DQC Reference Directory: /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference
[2024-01-24 11:36:21,888] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:36:21,889] [INFO] Task started: Prodigal
[2024-01-24 11:36:21,889] [INFO] Running command: gunzip -c /var/lib/cwl/stg67612440-b849-475b-8b9e-cf331a54d6b8/GCF_002777975.1_ASM277797v1_genomic.fna.gz | prodigal -d GCF_002777975.1_ASM277797v1_genomic.fna/cds.fna -a GCF_002777975.1_ASM277797v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:36:34,291] [INFO] Task succeeded: Prodigal
[2024-01-24 11:36:34,292] [INFO] Task started: HMMsearch
[2024-01-24 11:36:34,292] [INFO] Running command: hmmsearch --tblout GCF_002777975.1_ASM277797v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/reference_markers.hmm GCF_002777975.1_ASM277797v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:36:34,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:36:34,572] [INFO] Found 6/6 markers.
[2024-01-24 11:36:34,615] [INFO] Query marker FASTA was written to GCF_002777975.1_ASM277797v1_genomic.fna/markers.fasta
[2024-01-24 11:36:34,616] [INFO] Task started: Blastn
[2024-01-24 11:36:34,616] [INFO] Running command: blastn -query GCF_002777975.1_ASM277797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/reference_markers.fasta -out GCF_002777975.1_ASM277797v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:35,445] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:35,448] [INFO] Selected 15 target genomes.
[2024-01-24 11:36:35,448] [INFO] Target genome list was writen to GCF_002777975.1_ASM277797v1_genomic.fna/target_genomes.txt
[2024-01-24 11:36:35,487] [INFO] Task started: fastANI
[2024-01-24 11:36:35,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg67612440-b849-475b-8b9e-cf331a54d6b8/GCF_002777975.1_ASM277797v1_genomic.fna.gz --refList GCF_002777975.1_ASM277797v1_genomic.fna/target_genomes.txt --output GCF_002777975.1_ASM277797v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:36:50,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:50,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:36:50,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:36:50,342] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:36:50,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:36:50,342] [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 carassii	strain=08MAS2251	GCA_002777975.1	1987584	1987584	type	True	100.0	1434	1435	95	conclusive
Shewanella carassii	strain=CGMCC 1.16033	GCA_014644375.1	1987584	1987584	type	True	99.9893	1428	1435	95	conclusive
Shewanella algae	strain=CECT 5071	GCA_009183365.2	38313	38313	type	True	93.9044	1315	1435	95	below_threshold
Shewanella algae	strain=ATCC 51192	GCA_012396675.1	38313	38313	type	True	93.8582	1320	1435	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	93.8581	1268	1435	95	below_threshold
Shewanella indica	strain=KJW27	GCA_002836975.1	768528	768528	type	True	93.832	1221	1435	95	below_threshold
Shewanella indica	strain=KCTC 23171	GCA_014652115.1	768528	768528	type	True	93.7797	1230	1435	95	below_threshold
Shewanella chilikensis	strain=KCTC 22540	GCA_014651975.1	558541	558541	type	True	93.5559	1224	1435	95	below_threshold
Shewanella chilikensis	strain=JC5	GCA_003217175.1	558541	558541	type	True	93.5304	1224	1435	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	93.5292	1229	1435	95	below_threshold
Shewanella chilikensis	strain=JC5	GCA_002836945.1	558541	558541	type	True	93.4608	1210	1435	95	below_threshold
Shewanella jiangmenensis	strain=JM162201	GCA_018596335.1	2837387	2837387	type	True	78.6587	398	1435	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	78.5458	399	1435	95	below_threshold
Shewanella aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	78.3527	383	1435	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	78.2463	380	1435	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:36:50,344] [INFO] DFAST Taxonomy check result was written to GCF_002777975.1_ASM277797v1_genomic.fna/tc_result.tsv
[2024-01-24 11:36:50,344] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:36:50,344] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:36:50,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/checkm_data
[2024-01-24 11:36:50,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:36:50,387] [INFO] Task started: CheckM
[2024-01-24 11:36:50,387] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002777975.1_ASM277797v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002777975.1_ASM277797v1_genomic.fna/checkm_input GCF_002777975.1_ASM277797v1_genomic.fna/checkm_result
[2024-01-24 11:37:29,988] [INFO] Task succeeded: CheckM
[2024-01-24 11:37:29,989] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:37:30,007] [INFO] ===== Completeness check finished =====
[2024-01-24 11:37:30,008] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:37:30,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002777975.1_ASM277797v1_genomic.fna/markers.fasta)
[2024-01-24 11:37:30,008] [INFO] Task started: Blastn
[2024-01-24 11:37:30,009] [INFO] Running command: blastn -query GCF_002777975.1_ASM277797v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb647f2d2-fc2d-4810-977f-adfa37fc2bd9/dqc_reference/reference_markers_gtdb.fasta -out GCF_002777975.1_ASM277797v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:37:31,278] [INFO] Task succeeded: Blastn
[2024-01-24 11:37:31,282] [INFO] Selected 7 target genomes.
[2024-01-24 11:37:31,282] [INFO] Target genome list was writen to GCF_002777975.1_ASM277797v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:37:31,288] [INFO] Task started: fastANI
[2024-01-24 11:37:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg67612440-b849-475b-8b9e-cf331a54d6b8/GCF_002777975.1_ASM277797v1_genomic.fna.gz --refList GCF_002777975.1_ASM277797v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002777975.1_ASM277797v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:37:38,706] [INFO] Task succeeded: fastANI
[2024-01-24 11:37:38,718] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:37:38,718] [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_002777975.1	s__Shewanella carassii	100.0	1434	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_009183365.2	s__Shewanella algae	93.9015	1316	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
GCF_002836975.1	s__Shewanella indica	93.8331	1221	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.7827	98.42	98.01	0.95	0.93	6	-
GCF_002836945.1	s__Shewanella chilikensis	93.4551	1211	1435	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	79.1053	444	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_003353085.1	s__Shewanella corallii	78.6998	314	1435	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003957745.1	s__Shewanella khirikhana	78.6366	462	1435	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 11:37:38,720] [INFO] GTDB search result was written to GCF_002777975.1_ASM277797v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:37:38,720] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:37:38,723] [INFO] DFAST_QC result json was written to GCF_002777975.1_ASM277797v1_genomic.fna/dqc_result.json
[2024-01-24 11:37:38,724] [INFO] DFAST_QC completed!
[2024-01-24 11:37:38,724] [INFO] Total running time: 0h1m18s