[2023-03-18 22:26:05,789] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:26:05,789] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:26:05,789] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference
[2023-03-18 22:26:06,932] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:26:06,933] [INFO] Task started: Prodigal
[2023-03-18 22:26:06,933] [INFO] Running command: cat /var/lib/cwl/stgc8668a38-a316-4290-98d3-c1949289d525/OceanDNA-b35269.fa | prodigal -d OceanDNA-b35269/cds.fna -a OceanDNA-b35269/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:26:26,602] [INFO] Task succeeded: Prodigal
[2023-03-18 22:26:26,603] [INFO] Task started: HMMsearch
[2023-03-18 22:26:26,603] [INFO] Running command: hmmsearch --tblout OceanDNA-b35269/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/reference_markers.hmm OceanDNA-b35269/protein.faa > /dev/null
[2023-03-18 22:26:26,803] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:26:26,803] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc8668a38-a316-4290-98d3-c1949289d525/OceanDNA-b35269.fa]
[2023-03-18 22:26:26,827] [INFO] Query marker FASTA was written to OceanDNA-b35269/markers.fasta
[2023-03-18 22:26:26,830] [INFO] Task started: Blastn
[2023-03-18 22:26:26,830] [INFO] Running command: blastn -query OceanDNA-b35269/markers.fasta -db /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/reference_markers.fasta -out OceanDNA-b35269/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:26:27,426] [INFO] Task succeeded: Blastn
[2023-03-18 22:26:27,427] [INFO] Selected 10 target genomes.
[2023-03-18 22:26:27,428] [INFO] Target genome list was writen to OceanDNA-b35269/target_genomes.txt
[2023-03-18 22:26:27,433] [INFO] Task started: fastANI
[2023-03-18 22:26:27,433] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8668a38-a316-4290-98d3-c1949289d525/OceanDNA-b35269.fa --refList OceanDNA-b35269/target_genomes.txt --output OceanDNA-b35269/fastani_result.tsv --threads 1
[2023-03-18 22:26:37,557] [INFO] Task succeeded: fastANI
[2023-03-18 22:26:37,557] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:26:37,557] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:26:37,565] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 22:26:37,565] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 22:26:37,565] [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 aquimarina	strain=JCM 12193	GCA_023349185.1	260365	260365	type	True	95.494	1090	1143	95	conclusive
Shewanella loihica	strain=PV-4	GCA_000016065.1	359303	359303	type	True	89.1493	1073	1143	95	below_threshold
Shewanella insulae	strain=JBTF-M18	GCA_009831655.1	2681496	2681496	type	True	89.0628	1048	1143	95	below_threshold
Shewanella marisflavi	strain=JCM 12192	GCA_023283925.1	260364	260364	type	True	83.8992	916	1143	95	below_threshold
Shewanella colwelliana	strain=ATCC 39565	GCA_000518705.1	23	23	type	True	79.1794	428	1143	95	below_threshold
Shewanella algidipiscicola	strain=LMG 23746	GCA_003605125.1	614070	614070	type	True	78.9908	360	1143	95	below_threshold
Shewanella salipaludis	strain=SHSM-M6	GCA_012911865.1	2723052	2723052	type	True	77.7944	337	1143	95	below_threshold
Shewanella chilikensis	strain=CCUG 57101	GCA_023283475.1	558541	558541	type	True	77.6686	296	1143	95	below_threshold
Shewanella cyperi	strain=FJAT-53720	GCA_017354985.1	2814292	2814292	type	True	77.5975	284	1143	95	below_threshold
Shewanella algae	strain=NBRC 103173	GCA_001598875.1	38313	38313	type	True	77.5592	313	1143	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:26:37,565] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35269/tc_result.tsv
[2023-03-18 22:26:37,565] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:26:37,565] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:26:37,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/checkm_data
[2023-03-18 22:26:37,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:26:37,579] [INFO] Task started: CheckM
[2023-03-18 22:26:37,579] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35269/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35269/checkm_input OceanDNA-b35269/checkm_result
[2023-03-18 22:27:28,345] [INFO] Task succeeded: CheckM
[2023-03-18 22:27:28,346] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:27:28,432] [INFO] ===== Completeness check finished =====
[2023-03-18 22:27:28,433] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:27:28,433] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35269/markers.fasta)
[2023-03-18 22:27:28,434] [INFO] Task started: Blastn
[2023-03-18 22:27:28,434] [INFO] Running command: blastn -query OceanDNA-b35269/markers.fasta -db /var/lib/cwl/stg6d3826a4-84c8-40bc-b983-6715eab5b4b6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35269/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:27:29,527] [INFO] Task succeeded: Blastn
[2023-03-18 22:27:29,535] [INFO] Selected 9 target genomes.
[2023-03-18 22:27:29,535] [INFO] Target genome list was writen to OceanDNA-b35269/target_genomes_gtdb.txt
[2023-03-18 22:27:29,540] [INFO] Task started: fastANI
[2023-03-18 22:27:29,540] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8668a38-a316-4290-98d3-c1949289d525/OceanDNA-b35269.fa --refList OceanDNA-b35269/target_genomes_gtdb.txt --output OceanDNA-b35269/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:27:38,407] [INFO] Task succeeded: fastANI
[2023-03-18 22:27:38,413] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:27:38,413] [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_000832025.1	s__Shewanella sp000832025	97.4371	1112	1143	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	89.1493	1073	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	95.22	95.22	0.91	0.91	2	-
GCF_009831655.1	s__Shewanella insulae	89.0628	1048	1143	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	83.8074	925	1143	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	79.1794	428	1143	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	79.0119	360	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.64	98.64	0.92	0.92	2	-
GCF_012911865.1	s__Shewanella sp012911865	77.7937	339	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017354985.1	s__Shewanella sp017354985	77.6083	283	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	96.75	95.81	0.93	0.92	3	-
GCF_009183365.2	s__Shewanella algae	77.5743	321	1143	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	98.21	97.66	0.95	0.92	87	-
--------------------------------------------------------------------------------
[2023-03-18 22:27:38,416] [INFO] GTDB search result was written to OceanDNA-b35269/result_gtdb.tsv
[2023-03-18 22:27:38,419] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:27:38,422] [INFO] DFAST_QC result json was written to OceanDNA-b35269/dqc_result.json
[2023-03-18 22:27:38,422] [INFO] DFAST_QC completed!
[2023-03-18 22:27:38,422] [INFO] Total running time: 0h1m33s