[2023-03-18 09:26:42,704] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:26:42,713] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:26:42,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference
[2023-03-18 09:26:43,798] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:26:43,799] [INFO] Task started: Prodigal
[2023-03-18 09:26:43,799] [INFO] Running command: cat /var/lib/cwl/stg27efcc07-3723-4278-b743-eb48091ba3fd/OceanDNA-b8689.fa | prodigal -d OceanDNA-b8689/cds.fna -a OceanDNA-b8689/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:26:49,978] [INFO] Task succeeded: Prodigal
[2023-03-18 09:26:49,978] [INFO] Task started: HMMsearch
[2023-03-18 09:26:49,978] [INFO] Running command: hmmsearch --tblout OceanDNA-b8689/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/reference_markers.hmm OceanDNA-b8689/protein.faa > /dev/null
[2023-03-18 09:26:50,159] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:26:50,160] [INFO] Found 6/6 markers.
[2023-03-18 09:26:50,168] [INFO] Query marker FASTA was written to OceanDNA-b8689/markers.fasta
[2023-03-18 09:26:50,169] [INFO] Task started: Blastn
[2023-03-18 09:26:50,169] [INFO] Running command: blastn -query OceanDNA-b8689/markers.fasta -db /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/reference_markers.fasta -out OceanDNA-b8689/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:26:50,759] [INFO] Task succeeded: Blastn
[2023-03-18 09:26:50,760] [INFO] Selected 32 target genomes.
[2023-03-18 09:26:50,760] [INFO] Target genome list was writen to OceanDNA-b8689/target_genomes.txt
[2023-03-18 09:26:50,774] [INFO] Task started: fastANI
[2023-03-18 09:26:50,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg27efcc07-3723-4278-b743-eb48091ba3fd/OceanDNA-b8689.fa --refList OceanDNA-b8689/target_genomes.txt --output OceanDNA-b8689/fastani_result.tsv --threads 1
[2023-03-18 09:27:09,402] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:09,402] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:27:09,402] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:27:09,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:27:09,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:27:09,403] [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
--------------------------------------------------------------------------------
[2023-03-18 09:27:09,403] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8689/tc_result.tsv
[2023-03-18 09:27:09,403] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:27:09,403] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:27:09,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/checkm_data
[2023-03-18 09:27:09,405] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:27:09,408] [INFO] Task started: CheckM
[2023-03-18 09:27:09,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8689/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8689/checkm_input OceanDNA-b8689/checkm_result
[2023-03-18 09:27:30,394] [INFO] Task succeeded: CheckM
[2023-03-18 09:27:30,395] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:27:30,396] [INFO] ===== Completeness check finished =====
[2023-03-18 09:27:30,396] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:27:30,397] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8689/markers.fasta)
[2023-03-18 09:27:30,397] [INFO] Task started: Blastn
[2023-03-18 09:27:30,397] [INFO] Running command: blastn -query OceanDNA-b8689/markers.fasta -db /var/lib/cwl/stg9e9aeda1-3efc-497b-9961-378293685fbb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8689/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:27:31,415] [INFO] Task succeeded: Blastn
[2023-03-18 09:27:31,416] [INFO] Selected 20 target genomes.
[2023-03-18 09:27:31,416] [INFO] Target genome list was writen to OceanDNA-b8689/target_genomes_gtdb.txt
[2023-03-18 09:27:31,497] [INFO] Task started: fastANI
[2023-03-18 09:27:31,497] [INFO] Running command: fastANI --query /var/lib/cwl/stg27efcc07-3723-4278-b743-eb48091ba3fd/OceanDNA-b8689.fa --refList OceanDNA-b8689/target_genomes_gtdb.txt --output OceanDNA-b8689/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:27:37,530] [INFO] Task succeeded: fastANI
[2023-03-18 09:27:37,539] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:27:37,540] [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_902510415.1	s__MED-G13 sp902510415	97.3049	234	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	conclusive
GCA_902519075.1	s__MED-G13 sp902519075	80.1009	186	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	80.0775	201	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626365.1	s__MED-G13 sp902626365	79.9511	190	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_002702745.1	s__MED-G13 sp002702745	79.8995	178	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604715.1	s__MED-G13 sp902604715	79.6614	180	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902608795.1	s__MED-G13 sp902608795	79.6581	150	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902518355.1	s__MED-G13 sp902518355	79.5507	204	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.57	96.00	0.86	0.83	4	-
GCA_902557655.1	s__MED-G13 sp902557655	79.513	184	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_002691265.1	s__MED-G13 sp002691265	79.4545	187	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.61	95.49	0.82	0.79	4	-
GCA_902560045.1	s__MED-G13 sp902560045	79.325	141	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	-
GCA_902510475.1	s__MED-G13 sp902510475	79.2819	157	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626585.1	s__MED-G13 sp902626585	78.8602	197	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902512065.1	s__GCA-2700405 sp902512065	76.8003	73	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018657955.1	s__GCA-2700405 sp018657955	76.7515	70	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	99.95	99.87	0.95	0.89	9	-
GCA_002700405.1	s__GCA-2700405 sp002700405	76.7353	57	344	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2700405	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:27:37,540] [INFO] GTDB search result was written to OceanDNA-b8689/result_gtdb.tsv
[2023-03-18 09:27:37,540] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:27:37,541] [INFO] DFAST_QC result json was written to OceanDNA-b8689/dqc_result.json
[2023-03-18 09:27:37,541] [INFO] DFAST_QC completed!
[2023-03-18 09:27:37,541] [INFO] Total running time: 0h0m55s