[2023-03-17 23:39:58,853] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:39:58,853] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:39:58,853] [INFO] DQC Reference Directory: /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference
[2023-03-17 23:39:59,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:39:59,972] [INFO] Task started: Prodigal
[2023-03-17 23:39:59,973] [INFO] Running command: cat /var/lib/cwl/stgcf1177a0-35a7-44a0-8d77-2a8523dc070a/OceanDNA-b42156.fa | prodigal -d OceanDNA-b42156/cds.fna -a OceanDNA-b42156/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:40:06,170] [INFO] Task succeeded: Prodigal
[2023-03-17 23:40:06,170] [INFO] Task started: HMMsearch
[2023-03-17 23:40:06,170] [INFO] Running command: hmmsearch --tblout OceanDNA-b42156/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/reference_markers.hmm OceanDNA-b42156/protein.faa > /dev/null
[2023-03-17 23:40:06,351] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:40:06,352] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcf1177a0-35a7-44a0-8d77-2a8523dc070a/OceanDNA-b42156.fa]
[2023-03-17 23:40:06,363] [INFO] Query marker FASTA was written to OceanDNA-b42156/markers.fasta
[2023-03-17 23:40:06,364] [INFO] Task started: Blastn
[2023-03-17 23:40:06,364] [INFO] Running command: blastn -query OceanDNA-b42156/markers.fasta -db /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/reference_markers.fasta -out OceanDNA-b42156/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:07,069] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:07,070] [INFO] Selected 18 target genomes.
[2023-03-17 23:40:07,070] [INFO] Target genome list was writen to OceanDNA-b42156/target_genomes.txt
[2023-03-17 23:40:07,143] [INFO] Task started: fastANI
[2023-03-17 23:40:07,143] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf1177a0-35a7-44a0-8d77-2a8523dc070a/OceanDNA-b42156.fa --refList OceanDNA-b42156/target_genomes.txt --output OceanDNA-b42156/fastani_result.tsv --threads 1
[2023-03-17 23:40:14,306] [INFO] Task succeeded: fastANI
[2023-03-17 23:40:14,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:40:14,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:40:14,306] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:40:14,306] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:40:14,306] [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
--------------------------------------------------------------------------------
[2023-03-17 23:40:14,307] [INFO] DFAST Taxonomy check result was written to OceanDNA-b42156/tc_result.tsv
[2023-03-17 23:40:14,307] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:40:14,307] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:40:14,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/checkm_data
[2023-03-17 23:40:14,355] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:40:14,358] [INFO] Task started: CheckM
[2023-03-17 23:40:14,358] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b42156/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b42156/checkm_input OceanDNA-b42156/checkm_result
[2023-03-17 23:40:39,448] [INFO] Task succeeded: CheckM
[2023-03-17 23:40:39,448] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:40:39,450] [INFO] ===== Completeness check finished =====
[2023-03-17 23:40:39,450] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:40:39,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b42156/markers.fasta)
[2023-03-17 23:40:39,451] [INFO] Task started: Blastn
[2023-03-17 23:40:39,451] [INFO] Running command: blastn -query OceanDNA-b42156/markers.fasta -db /var/lib/cwl/stg6e12b99d-1709-4c97-bfb6-3f21a5dc3b9f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b42156/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:40,719] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:40,720] [INFO] Selected 17 target genomes.
[2023-03-17 23:40:40,720] [INFO] Target genome list was writen to OceanDNA-b42156/target_genomes_gtdb.txt
[2023-03-17 23:40:40,792] [INFO] Task started: fastANI
[2023-03-17 23:40:40,792] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf1177a0-35a7-44a0-8d77-2a8523dc070a/OceanDNA-b42156.fa --refList OceanDNA-b42156/target_genomes_gtdb.txt --output OceanDNA-b42156/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:40:44,955] [INFO] Task succeeded: fastANI
[2023-03-17 23:40:44,965] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:40:44,966] [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_902511575.1	s__D2472 sp902511575	79.5332	190	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307935.1	s__D2472 sp000307935	79.2995	158	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902513515.1	s__D2472 sp902513515	79.2163	140	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512655.1	s__D2472 sp902512655	79.1863	134	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284215.1	s__D2472 sp003284215	79.1749	180	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.26	97.20	0.81	0.71	5	-
GCA_902596165.1	s__D2472 sp902596165	79.1005	172	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779505.1	s__D2472 sp016779505	79.0826	153	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.99	98.50	0.76	0.70	3	-
GCA_902511425.1	s__D2472 sp902511425	78.9461	135	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902595065.1	s__D2472 sp902595065	78.8478	200	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	98.09	97.88	0.94	0.91	4	-
GCA_905181595.1	s__D2472 sp905181595	78.7923	179	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902602595.1	s__D2472 sp902602595	78.6709	163	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902593675.1	s__D2472 sp902593675	78.5869	186	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331545.1	s__D2472 sp003331545	78.5655	100	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623685.1	s__D2472 sp902623685	78.1522	132	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	99.90	99.90	0.83	0.83	2	-
GCA_902528215.1	s__D2472 sp902528215	77.7553	117	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902541245.1	s__D2472 sp902541245	77.7007	102	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902608115.1	s__D2472 sp902608115	77.2172	104	379	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SAR86;f__D2472;g__D2472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:40:44,966] [INFO] GTDB search result was written to OceanDNA-b42156/result_gtdb.tsv
[2023-03-17 23:40:44,966] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:40:44,967] [INFO] DFAST_QC result json was written to OceanDNA-b42156/dqc_result.json
[2023-03-17 23:40:44,968] [INFO] DFAST_QC completed!
[2023-03-17 23:40:44,968] [INFO] Total running time: 0h0m46s