[2023-03-14 11:40:05,568] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:40:05,568] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:40:05,569] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference
[2023-03-14 11:40:06,682] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:40:06,682] [INFO] Task started: Prodigal
[2023-03-14 11:40:06,683] [INFO] Running command: cat /var/lib/cwl/stg8384f0a7-d39a-4cfc-87a7-ce2bf4db6044/OceanDNA-b7642.fa | prodigal -d OceanDNA-b7642/cds.fna -a OceanDNA-b7642/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:40:14,775] [INFO] Task succeeded: Prodigal
[2023-03-14 11:40:14,775] [INFO] Task started: HMMsearch
[2023-03-14 11:40:14,775] [INFO] Running command: hmmsearch --tblout OceanDNA-b7642/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/reference_markers.hmm OceanDNA-b7642/protein.faa > /dev/null
[2023-03-14 11:40:14,954] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:40:14,954] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8384f0a7-d39a-4cfc-87a7-ce2bf4db6044/OceanDNA-b7642.fa]
[2023-03-14 11:40:14,977] [INFO] Query marker FASTA was written to OceanDNA-b7642/markers.fasta
[2023-03-14 11:40:14,978] [INFO] Task started: Blastn
[2023-03-14 11:40:14,978] [INFO] Running command: blastn -query OceanDNA-b7642/markers.fasta -db /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/reference_markers.fasta -out OceanDNA-b7642/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:15,500] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:15,502] [INFO] Selected 30 target genomes.
[2023-03-14 11:40:15,502] [INFO] Target genome list was writen to OceanDNA-b7642/target_genomes.txt
[2023-03-14 11:40:15,521] [INFO] Task started: fastANI
[2023-03-14 11:40:15,521] [INFO] Running command: fastANI --query /var/lib/cwl/stg8384f0a7-d39a-4cfc-87a7-ce2bf4db6044/OceanDNA-b7642.fa --refList OceanDNA-b7642/target_genomes.txt --output OceanDNA-b7642/fastani_result.tsv --threads 1
[2023-03-14 11:40:31,516] [INFO] Task succeeded: fastANI
[2023-03-14 11:40:31,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:40:31,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:40:31,517] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:40:31,517] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:40:31,517] [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
--------------------------------------------------------------------------------
[2023-03-14 11:40:31,519] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7642/tc_result.tsv
[2023-03-14 11:40:31,522] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:40:31,522] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:40:31,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/checkm_data
[2023-03-14 11:40:31,525] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:40:31,531] [INFO] Task started: CheckM
[2023-03-14 11:40:31,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7642/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7642/checkm_input OceanDNA-b7642/checkm_result
[2023-03-14 11:40:56,952] [INFO] Task succeeded: CheckM
[2023-03-14 11:40:56,952] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.56%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:40:56,976] [INFO] ===== Completeness check finished =====
[2023-03-14 11:40:56,976] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:40:56,976] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7642/markers.fasta)
[2023-03-14 11:40:56,977] [INFO] Task started: Blastn
[2023-03-14 11:40:56,977] [INFO] Running command: blastn -query OceanDNA-b7642/markers.fasta -db /var/lib/cwl/stg1dbbd240-633a-4f7e-a43e-0be670d2e4b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7642/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:40:57,674] [INFO] Task succeeded: Blastn
[2023-03-14 11:40:57,729] [INFO] Selected 18 target genomes.
[2023-03-14 11:40:57,730] [INFO] Target genome list was writen to OceanDNA-b7642/target_genomes_gtdb.txt
[2023-03-14 11:40:57,741] [INFO] Task started: fastANI
[2023-03-14 11:40:57,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg8384f0a7-d39a-4cfc-87a7-ce2bf4db6044/OceanDNA-b7642.fa --refList OceanDNA-b7642/target_genomes_gtdb.txt --output OceanDNA-b7642/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:41:02,528] [INFO] Task succeeded: fastANI
[2023-03-14 11:41:02,536] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 11:41:02,536] [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_902523635.1	s__MAG-121220-bin8 sp902523635	91.5242	253	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705485.1	s__MAG-121220-bin8 sp002705485	78.5184	171	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.79	97.60	0.73	0.71	4	-
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	76.7108	53	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	76.5744	123	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	76.5357	84	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	76.5209	75	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	76.4686	85	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	76.3118	92	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	76.2784	59	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	76.2735	71	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	76.1556	64	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	76.1473	64	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	75.7532	80	407	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 11:41:02,538] [INFO] GTDB search result was written to OceanDNA-b7642/result_gtdb.tsv
[2023-03-14 11:41:02,539] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:41:02,540] [INFO] DFAST_QC result json was written to OceanDNA-b7642/dqc_result.json
[2023-03-14 11:41:02,541] [INFO] DFAST_QC completed!
[2023-03-14 11:41:02,541] [INFO] Total running time: 0h0m57s