[2023-03-16 10:00:16,249] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:00:16,249] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:00:16,249] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference
[2023-03-16 10:00:17,351] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:00:17,351] [INFO] Task started: Prodigal
[2023-03-16 10:00:17,351] [INFO] Running command: cat /var/lib/cwl/stg6ac3f1bc-b2d6-4c2c-b572-00fe52b6f431/OceanDNA-b35250.fa | prodigal -d OceanDNA-b35250/cds.fna -a OceanDNA-b35250/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:00:30,081] [INFO] Task succeeded: Prodigal
[2023-03-16 10:00:30,082] [INFO] Task started: HMMsearch
[2023-03-16 10:00:30,082] [INFO] Running command: hmmsearch --tblout OceanDNA-b35250/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/reference_markers.hmm OceanDNA-b35250/protein.faa > /dev/null
[2023-03-16 10:00:30,287] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:00:30,288] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6ac3f1bc-b2d6-4c2c-b572-00fe52b6f431/OceanDNA-b35250.fa]
[2023-03-16 10:00:30,312] [INFO] Query marker FASTA was written to OceanDNA-b35250/markers.fasta
[2023-03-16 10:00:30,313] [INFO] Task started: Blastn
[2023-03-16 10:00:30,313] [INFO] Running command: blastn -query OceanDNA-b35250/markers.fasta -db /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/reference_markers.fasta -out OceanDNA-b35250/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:00:30,899] [INFO] Task succeeded: Blastn
[2023-03-16 10:00:30,901] [INFO] Selected 11 target genomes.
[2023-03-16 10:00:30,901] [INFO] Target genome list was writen to OceanDNA-b35250/target_genomes.txt
[2023-03-16 10:00:30,907] [INFO] Task started: fastANI
[2023-03-16 10:00:30,907] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac3f1bc-b2d6-4c2c-b572-00fe52b6f431/OceanDNA-b35250.fa --refList OceanDNA-b35250/target_genomes.txt --output OceanDNA-b35250/fastani_result.tsv --threads 1
[2023-03-16 10:00:41,375] [INFO] Task succeeded: fastANI
[2023-03-16 10:00:41,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:00:41,376] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:00:41,383] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 10:00:41,383] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 10:00:41,384] [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 basaltis	strain=KCTC 22121	GCA_023283885.1	472183	472183	type	True	99.0396	673	691	95	conclusive
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	84.8837	591	691	95	below_threshold
Shewanella inventionis	strain=CGMCC 1.15339	GCA_014641855.1	1738770	1738770	type	True	84.8258	595	691	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_014648335.1	2282700	2282700	type	True	84.8002	592	691	95	below_threshold
Shewanella litoralis	strain=JCM 32306	GCA_009828585.1	2282700	2282700	type	True	84.7669	601	691	95	below_threshold
Shewanella saliphila	strain=KCTC 62131	GCA_023283695.1	2282698	2282698	type	True	83.8532	565	691	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	83.8325	601	691	95	below_threshold
Shewanella saliphila	strain=JCM 32304	GCA_014648295.1	2282698	2282698	type	True	83.8167	567	691	95	below_threshold
Shewanella ulleungensis	strain=JCM 32305	GCA_014648315.1	2282699	2282699	type	True	83.8141	608	691	95	below_threshold
Shewanella algicola	strain=JCM 31091	GCA_014648035.1	640633	640633	type	True	83.7005	549	691	95	below_threshold
Shewanella psychromarinicola	strain=M2	GCA_003855155.1	2487742	2487742	type	True	80.1625	400	691	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:00:41,385] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35250/tc_result.tsv
[2023-03-16 10:00:41,385] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:00:41,385] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:00:41,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/checkm_data
[2023-03-16 10:00:41,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:00:41,474] [INFO] Task started: CheckM
[2023-03-16 10:00:41,474] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35250/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35250/checkm_input OceanDNA-b35250/checkm_result
[2023-03-16 10:01:18,289] [INFO] Task succeeded: CheckM
[2023-03-16 10:01:18,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.42%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:01:18,295] [INFO] ===== Completeness check finished =====
[2023-03-16 10:01:18,295] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:01:18,296] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35250/markers.fasta)
[2023-03-16 10:01:18,297] [INFO] Task started: Blastn
[2023-03-16 10:01:18,297] [INFO] Running command: blastn -query OceanDNA-b35250/markers.fasta -db /var/lib/cwl/stg7e497094-e601-4e1a-89f0-c01fbad8a48f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35250/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:01:19,188] [INFO] Task succeeded: Blastn
[2023-03-16 10:01:19,191] [INFO] Selected 6 target genomes.
[2023-03-16 10:01:19,191] [INFO] Target genome list was writen to OceanDNA-b35250/target_genomes_gtdb.txt
[2023-03-16 10:01:19,197] [INFO] Task started: fastANI
[2023-03-16 10:01:19,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg6ac3f1bc-b2d6-4c2c-b572-00fe52b6f431/OceanDNA-b35250.fa --refList OceanDNA-b35250/target_genomes_gtdb.txt --output OceanDNA-b35250/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:01:24,622] [INFO] Task succeeded: fastANI
[2023-03-16 10:01:24,626] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:01:24,626] [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_014641855.1	s__Shewanella inventionis	84.821	596	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009828585.1	s__Shewanella litoralis	84.7669	601	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014648315.1	s__Shewanella ulleungensis	83.8243	608	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648295.1	s__Shewanella saliphila	83.7894	569	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_014648035.1	s__Shewanella algicola	83.7063	549	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.1181	N/A	N/A	N/A	N/A	1	-
GCF_006385555.1	s__Shewanella polaris	80.4975	412	691	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	97.84	97.84	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2023-03-16 10:01:24,628] [INFO] GTDB search result was written to OceanDNA-b35250/result_gtdb.tsv
[2023-03-16 10:01:24,628] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:01:24,630] [INFO] DFAST_QC result json was written to OceanDNA-b35250/dqc_result.json
[2023-03-16 10:01:24,630] [INFO] DFAST_QC completed!
[2023-03-16 10:01:24,630] [INFO] Total running time: 0h1m8s