[2024-01-25 18:51:35,768] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:51:35,769] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:51:35,769] [INFO] DQC Reference Directory: /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference
[2024-01-25 18:51:36,900] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:51:36,901] [INFO] Task started: Prodigal
[2024-01-25 18:51:36,901] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c4feb17-f70d-4549-8cc7-9936e497e07b/GCF_014647575.1_ASM1464757v1_genomic.fna.gz | prodigal -d GCF_014647575.1_ASM1464757v1_genomic.fna/cds.fna -a GCF_014647575.1_ASM1464757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:51:47,937] [INFO] Task succeeded: Prodigal
[2024-01-25 18:51:47,937] [INFO] Task started: HMMsearch
[2024-01-25 18:51:47,938] [INFO] Running command: hmmsearch --tblout GCF_014647575.1_ASM1464757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/reference_markers.hmm GCF_014647575.1_ASM1464757v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:51:48,226] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:51:48,227] [INFO] Found 6/6 markers.
[2024-01-25 18:51:48,278] [INFO] Query marker FASTA was written to GCF_014647575.1_ASM1464757v1_genomic.fna/markers.fasta
[2024-01-25 18:51:48,278] [INFO] Task started: Blastn
[2024-01-25 18:51:48,278] [INFO] Running command: blastn -query GCF_014647575.1_ASM1464757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/reference_markers.fasta -out GCF_014647575.1_ASM1464757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:48,981] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:48,984] [INFO] Selected 12 target genomes.
[2024-01-25 18:51:48,984] [INFO] Target genome list was writen to GCF_014647575.1_ASM1464757v1_genomic.fna/target_genomes.txt
[2024-01-25 18:51:48,998] [INFO] Task started: fastANI
[2024-01-25 18:51:48,998] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4feb17-f70d-4549-8cc7-9936e497e07b/GCF_014647575.1_ASM1464757v1_genomic.fna.gz --refList GCF_014647575.1_ASM1464757v1_genomic.fna/target_genomes.txt --output GCF_014647575.1_ASM1464757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:52:03,115] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:03,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:52:03,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:52:03,125] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:52:03,125] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:52:03,125] [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 hanedai	strain=JCM 20706	GCA_014647575.1	25	25	type	True	100.0	1907	1920	95	conclusive
Shewanella hanedai	strain=JCM 20706	GCA_007197645.1	25	25	type	True	99.9886	1910	1920	95	conclusive
Shewanella woodyi	strain=ATCC 51908	GCA_000019525.1	60961	60961	type	True	80.9712	1062	1920	95	below_threshold
Shewanella nanhaiensis	strain=NR704-98	GCA_019457885.1	2864872	2864872	type	True	80.9367	1030	1920	95	below_threshold
Shewanella sediminis	strain=HAW-EB3	GCA_000018025.1	271097	271097	type	True	79.6844	563	1920	95	below_threshold
Shewanella canadensis	strain=HAW-EB2	GCA_003966225.1	271096	271096	type	True	79.6628	573	1920	95	below_threshold
Shewanella atlantica	strain=HAW-EB5	GCA_003966265.1	271099	271099	type	True	79.445	553	1920	95	below_threshold
Shewanella psychrophila	strain=WP2	GCA_002005305.1	225848	225848	type	True	78.8265	527	1920	95	below_threshold
Shewanella marinintestina	strain=LMG 21403	GCA_023283845.1	190305	190305	type	True	78.7113	363	1920	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	78.4991	171	1920	95	below_threshold
Shewanella olleyana	strain=LMG 21437	GCA_023283825.1	135626	135626	type	True	77.706	242	1920	95	below_threshold
Parashewanella hymeniacidonis	strain=202IG2-18	GCA_016900895.1	2807618	2807618	type	True	77.5515	131	1920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:52:03,126] [INFO] DFAST Taxonomy check result was written to GCF_014647575.1_ASM1464757v1_genomic.fna/tc_result.tsv
[2024-01-25 18:52:03,127] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:52:03,127] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:52:03,127] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/checkm_data
[2024-01-25 18:52:03,128] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:52:03,209] [INFO] Task started: CheckM
[2024-01-25 18:52:03,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014647575.1_ASM1464757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014647575.1_ASM1464757v1_genomic.fna/checkm_input GCF_014647575.1_ASM1464757v1_genomic.fna/checkm_result
[2024-01-25 18:52:39,127] [INFO] Task succeeded: CheckM
[2024-01-25 18:52:39,128] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:52:39,145] [INFO] ===== Completeness check finished =====
[2024-01-25 18:52:39,146] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:52:39,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014647575.1_ASM1464757v1_genomic.fna/markers.fasta)
[2024-01-25 18:52:39,146] [INFO] Task started: Blastn
[2024-01-25 18:52:39,146] [INFO] Running command: blastn -query GCF_014647575.1_ASM1464757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfddcfd4c-35f5-4e6f-9c4f-8fa26f7036cd/dqc_reference/reference_markers_gtdb.fasta -out GCF_014647575.1_ASM1464757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:40,224] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:40,227] [INFO] Selected 11 target genomes.
[2024-01-25 18:52:40,227] [INFO] Target genome list was writen to GCF_014647575.1_ASM1464757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:52:40,244] [INFO] Task started: fastANI
[2024-01-25 18:52:40,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c4feb17-f70d-4549-8cc7-9936e497e07b/GCF_014647575.1_ASM1464757v1_genomic.fna.gz --refList GCF_014647575.1_ASM1464757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014647575.1_ASM1464757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:52:53,643] [INFO] Task succeeded: fastANI
[2024-01-25 18:52:53,652] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:52:53,652] [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_007197645.1	s__Shewanella hanedai	99.9886	1910	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000019525.1	s__Shewanella woodyi	80.9872	1061	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.96	97.96	0.94	0.94	2	-
GCF_003966225.1	s__Shewanella canadensis	79.699	567	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000018025.1	s__Shewanella sediminis	79.6535	565	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013248905.1	s__Shewanella sp013248905	79.5154	616	1920	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	79.4384	552	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004545.2	s__Shewanella sp007004545	79.2033	558	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.97	99.97	0.99	0.99	2	-
GCF_001957125.1	s__Shewanella sp001957125	79.1781	509	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016757755.1	s__Shewanella sp016757755	78.8591	343	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005305.1	s__Shewanella psychrophila	78.8261	527	1920	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	78.7927	426	1920	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:52:53,653] [INFO] GTDB search result was written to GCF_014647575.1_ASM1464757v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:52:53,654] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:52:53,657] [INFO] DFAST_QC result json was written to GCF_014647575.1_ASM1464757v1_genomic.fna/dqc_result.json
[2024-01-25 18:52:53,657] [INFO] DFAST_QC completed!
[2024-01-25 18:52:53,657] [INFO] Total running time: 0h1m18s