[2023-03-16 00:19:47,508] [INFO] DFAST_QC pipeline started.
[2023-03-16 00:19:47,509] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 00:19:47,509] [INFO] DQC Reference Directory: /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference
[2023-03-16 00:19:48,639] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 00:19:48,639] [INFO] Task started: Prodigal
[2023-03-16 00:19:48,639] [INFO] Running command: cat /var/lib/cwl/stge0ab20ad-7598-48b5-b258-3a87264f789e/OceanDNA-b42402.fa | prodigal -d OceanDNA-b42402/cds.fna -a OceanDNA-b42402/protein.faa -g 11 -q > /dev/null
[2023-03-16 00:19:53,326] [INFO] Task succeeded: Prodigal
[2023-03-16 00:19:53,326] [INFO] Task started: HMMsearch
[2023-03-16 00:19:53,326] [INFO] Running command: hmmsearch --tblout OceanDNA-b42402/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/reference_markers.hmm OceanDNA-b42402/protein.faa > /dev/null
[2023-03-16 00:19:53,479] [INFO] Task succeeded: HMMsearch
[2023-03-16 00:19:53,480] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge0ab20ad-7598-48b5-b258-3a87264f789e/OceanDNA-b42402.fa]
[2023-03-16 00:19:53,489] [INFO] Query marker FASTA was written to OceanDNA-b42402/markers.fasta
[2023-03-16 00:19:53,490] [INFO] Task started: Blastn
[2023-03-16 00:19:53,490] [INFO] Running command: blastn -query OceanDNA-b42402/markers.fasta -db /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/reference_markers.fasta -out OceanDNA-b42402/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:19:54,026] [INFO] Task succeeded: Blastn
[2023-03-16 00:19:54,028] [INFO] Selected 24 target genomes.
[2023-03-16 00:19:54,028] [INFO] Target genome list was writen to OceanDNA-b42402/target_genomes.txt
[2023-03-16 00:19:54,042] [INFO] Task started: fastANI
[2023-03-16 00:19:54,042] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ab20ad-7598-48b5-b258-3a87264f789e/OceanDNA-b42402.fa --refList OceanDNA-b42402/target_genomes.txt --output OceanDNA-b42402/fastani_result.tsv --threads 1
[2023-03-16 00:20:03,871] [INFO] Task succeeded: fastANI
[2023-03-16 00:20:03,872] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 00:20:03,872] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 00:20:03,872] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 00:20:03,872] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 00:20:03,872] [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
--------------------------------------------------------------------------------
[2023-03-16 00:20:03,873] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42402/tc_result.tsv
[2023-03-16 00:20:03,873] [INFO] ===== Taxonomy check completed =====
[2023-03-16 00:20:03,873] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 00:20:03,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/checkm_data
[2023-03-16 00:20:03,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 00:20:03,879] [INFO] Task started: CheckM
[2023-03-16 00:20:03,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42402/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42402/checkm_input OceanDNA-b42402/checkm_result
[2023-03-16 00:20:21,530] [INFO] Task succeeded: CheckM
[2023-03-16 00:20:21,530] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 00:20:21,534] [INFO] ===== Completeness check finished =====
[2023-03-16 00:20:21,534] [INFO] ===== Start GTDB Search =====
[2023-03-16 00:20:21,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42402/markers.fasta)
[2023-03-16 00:20:21,535] [INFO] Task started: Blastn
[2023-03-16 00:20:21,535] [INFO] Running command: blastn -query OceanDNA-b42402/markers.fasta -db /var/lib/cwl/stg182f44f4-3ef9-4445-affa-f72fe8988810/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42402/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 00:20:22,395] [INFO] Task succeeded: Blastn
[2023-03-16 00:20:22,399] [INFO] Selected 12 target genomes.
[2023-03-16 00:20:22,399] [INFO] Target genome list was writen to OceanDNA-b42402/target_genomes_gtdb.txt
[2023-03-16 00:20:22,406] [INFO] Task started: fastANI
[2023-03-16 00:20:22,406] [INFO] Running command: fastANI --query /var/lib/cwl/stge0ab20ad-7598-48b5-b258-3a87264f789e/OceanDNA-b42402.fa --refList OceanDNA-b42402/target_genomes_gtdb.txt --output OceanDNA-b42402/fastani_result_gtdb.tsv --threads 1
[2023-03-16 00:20:24,710] [INFO] Task succeeded: fastANI
[2023-03-16 00:20:24,717] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 00:20:24,717] [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
GCA_000385055.1	s__SCGC-AAA076-P13 sp000385055	91.4712	271	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.19	98.19	0.89	0.89	2	-
GCA_902557705.1	s__SCGC-AAA076-P13 sp902557705	79.638	133	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591665.1	s__SCGC-AAA076-P13 sp902591665	79.6098	154	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	99.81	99.81	0.85	0.85	2	-
GCA_010024215.1	s__SCGC-AAA076-P13 sp010024215	79.4981	124	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	98.04	96.58	0.74	0.68	5	-
GCA_902558395.1	s__SCGC-AAA076-P13 sp902558395	79.4854	189	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.77	97.77	0.94	0.94	2	-
GCA_902635645.1	s__SCGC-AAA076-P13 sp902635645	79.3193	130	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	97.13	97.13	0.67	0.67	2	-
GCA_902610905.1	s__SCGC-AAA076-P13 sp902610905	79.3105	131	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902556355.1	s__SCGC-AAA076-P13 sp902556355	79.2513	135	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902558375.1	s__SCGC-AAA076-P13 sp902558375	79.0928	134	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591565.1	s__SCGC-AAA076-P13 sp902591565	78.6222	146	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384935.1	s__SCGC-AAA076-P13 sp000384935	78.0128	124	312	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__SCGC-AAA076-P13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 00:20:24,718] [INFO] GTDB search result was written to OceanDNA-b42402/result_gtdb.tsv
[2023-03-16 00:20:24,718] [INFO] ===== GTDB Search completed =====
[2023-03-16 00:20:24,719] [INFO] DFAST_QC result json was written to OceanDNA-b42402/dqc_result.json
[2023-03-16 00:20:24,719] [INFO] DFAST_QC completed!
[2023-03-16 00:20:24,719] [INFO] Total running time: 0h0m37s