[2023-03-18 07:29:30,335] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,335] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,336] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference
[2023-03-18 07:29:31,934] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg3996cbb5-8b15-47af-ab72-debc6aad4995/OceanDNA-b34949.fa | prodigal -d OceanDNA-b34949/cds.fna -a OceanDNA-b34949/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:56,184] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:56,185] [INFO] Task started: HMMsearch
[2023-03-18 07:29:56,185] [INFO] Running command: hmmsearch --tblout OceanDNA-b34949/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/reference_markers.hmm OceanDNA-b34949/protein.faa > /dev/null
[2023-03-18 07:29:56,444] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:56,445] [INFO] Found 6/6 markers.
[2023-03-18 07:29:56,475] [INFO] Query marker FASTA was written to OceanDNA-b34949/markers.fasta
[2023-03-18 07:29:56,475] [INFO] Task started: Blastn
[2023-03-18 07:29:56,475] [INFO] Running command: blastn -query OceanDNA-b34949/markers.fasta -db /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/reference_markers.fasta -out OceanDNA-b34949/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:57,134] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:57,135] [INFO] Selected 9 target genomes.
[2023-03-18 07:29:57,135] [INFO] Target genome list was writen to OceanDNA-b34949/target_genomes.txt
[2023-03-18 07:29:57,138] [INFO] Task started: fastANI
[2023-03-18 07:29:57,138] [INFO] Running command: fastANI --query /var/lib/cwl/stg3996cbb5-8b15-47af-ab72-debc6aad4995/OceanDNA-b34949.fa --refList OceanDNA-b34949/target_genomes.txt --output OceanDNA-b34949/fastani_result.tsv --threads 1
[2023-03-18 07:30:06,203] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:06,203] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:30:06,203] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:30:06,209] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 07:30:06,209] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:30:06,209] [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
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	97.4007	1285	1500	95	conclusive
Pseudoalteromonas ostreae	strain=hOe-66	GCA_018069805.1	2774154	2774154	type	True	93.4659	1124	1500	95	below_threshold
Pseudoalteromonas prydzensis	strain=DSM 14232	GCA_001661495.1	182141	182141	type	True	85.3771	1112	1500	95	below_threshold
Pseudoalteromonas prydzensis	strain=ACAM 620	GCA_014925355.1	182141	182141	type	True	85.3569	1114	1500	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	82.8923	858	1500	95	below_threshold
Pseudoalteromonas distincta	strain=ATCC 700518	GCA_000814675.1	77608	77608	type	True	80.3174	550	1500	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:30:06,209] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34949/tc_result.tsv
[2023-03-18 07:30:06,209] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:30:06,209] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:30:06,210] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/checkm_data
[2023-03-18 07:30:06,210] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:30:06,218] [INFO] Task started: CheckM
[2023-03-18 07:30:06,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34949/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34949/checkm_input OceanDNA-b34949/checkm_result
[2023-03-18 07:31:06,178] [INFO] Task succeeded: CheckM
[2023-03-18 07:31:06,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.43%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:31:06,181] [INFO] ===== Completeness check finished =====
[2023-03-18 07:31:06,182] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:31:06,182] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34949/markers.fasta)
[2023-03-18 07:31:06,182] [INFO] Task started: Blastn
[2023-03-18 07:31:06,182] [INFO] Running command: blastn -query OceanDNA-b34949/markers.fasta -db /var/lib/cwl/stg7b1387eb-1be3-4512-9e16-227d1e324a35/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34949/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:31:07,244] [INFO] Task succeeded: Blastn
[2023-03-18 07:31:07,245] [INFO] Selected 6 target genomes.
[2023-03-18 07:31:07,245] [INFO] Target genome list was writen to OceanDNA-b34949/target_genomes_gtdb.txt
[2023-03-18 07:31:07,301] [INFO] Task started: fastANI
[2023-03-18 07:31:07,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg3996cbb5-8b15-47af-ab72-debc6aad4995/OceanDNA-b34949.fa --refList OceanDNA-b34949/target_genomes_gtdb.txt --output OceanDNA-b34949/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:31:14,569] [INFO] Task succeeded: fastANI
[2023-03-18 07:31:14,574] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:31:14,574] [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_902498845.1	s__Pseudoalteromonas rhizosphaerae	97.4138	1284	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.81	97.24	0.86	0.81	17	conclusive
GCF_018069805.1	s__Pseudoalteromonas sp018069805	93.4541	1125	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927645.1	s__Pseudoalteromonas arctica_A	91.9747	982	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050055.1	s__Pseudoalteromonas prydzensis_A	87.4841	1078	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001661495.1	s__Pseudoalteromonas prydzensis	85.3838	1111	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.53	97.08	0.91	0.82	3	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	82.9266	852	1500	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-18 07:31:14,574] [INFO] GTDB search result was written to OceanDNA-b34949/result_gtdb.tsv
[2023-03-18 07:31:14,574] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:31:14,575] [INFO] DFAST_QC result json was written to OceanDNA-b34949/dqc_result.json
[2023-03-18 07:31:14,575] [INFO] DFAST_QC completed!
[2023-03-18 07:31:14,575] [INFO] Total running time: 0h1m44s