[2023-03-16 10:06:33,505] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:06:33,505] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:06:33,505] [INFO] DQC Reference Directory: /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference
[2023-03-16 10:06:34,661] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:06:34,662] [INFO] Task started: Prodigal
[2023-03-16 10:06:34,662] [INFO] Running command: cat /var/lib/cwl/stga850e0d9-4757-4328-908c-f759d5658491/OceanDNA-b4880.fa | prodigal -d OceanDNA-b4880/cds.fna -a OceanDNA-b4880/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:06:41,593] [INFO] Task succeeded: Prodigal
[2023-03-16 10:06:41,594] [INFO] Task started: HMMsearch
[2023-03-16 10:06:41,594] [INFO] Running command: hmmsearch --tblout OceanDNA-b4880/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/reference_markers.hmm OceanDNA-b4880/protein.faa > /dev/null
[2023-03-16 10:06:41,744] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:06:41,744] [INFO] Found 6/6 markers.
[2023-03-16 10:06:41,754] [INFO] Query marker FASTA was written to OceanDNA-b4880/markers.fasta
[2023-03-16 10:06:41,756] [INFO] Task started: Blastn
[2023-03-16 10:06:41,756] [INFO] Running command: blastn -query OceanDNA-b4880/markers.fasta -db /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/reference_markers.fasta -out OceanDNA-b4880/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:06:42,367] [INFO] Task succeeded: Blastn
[2023-03-16 10:06:42,368] [INFO] Selected 25 target genomes.
[2023-03-16 10:06:42,369] [INFO] Target genome list was writen to OceanDNA-b4880/target_genomes.txt
[2023-03-16 10:06:42,386] [INFO] Task started: fastANI
[2023-03-16 10:06:42,386] [INFO] Running command: fastANI --query /var/lib/cwl/stga850e0d9-4757-4328-908c-f759d5658491/OceanDNA-b4880.fa --refList OceanDNA-b4880/target_genomes.txt --output OceanDNA-b4880/fastani_result.tsv --threads 1
[2023-03-16 10:06:55,434] [INFO] Task succeeded: fastANI
[2023-03-16 10:06:55,435] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:06:55,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:06:55,435] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:06:55,435] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 10:06:55,435] [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 10:06:55,435] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4880/tc_result.tsv
[2023-03-16 10:06:55,436] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:06:55,436] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:06:55,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/checkm_data
[2023-03-16 10:06:55,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:06:55,441] [INFO] Task started: CheckM
[2023-03-16 10:06:55,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4880/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4880/checkm_input OceanDNA-b4880/checkm_result
[2023-03-16 10:07:17,965] [INFO] Task succeeded: CheckM
[2023-03-16 10:07:17,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:07:17,967] [INFO] ===== Completeness check finished =====
[2023-03-16 10:07:17,967] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:07:17,967] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4880/markers.fasta)
[2023-03-16 10:07:17,968] [INFO] Task started: Blastn
[2023-03-16 10:07:17,968] [INFO] Running command: blastn -query OceanDNA-b4880/markers.fasta -db /var/lib/cwl/stge330a271-68f8-40b9-a230-f3b2269f4cdc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4880/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:07:18,904] [INFO] Task succeeded: Blastn
[2023-03-16 10:07:18,905] [INFO] Selected 23 target genomes.
[2023-03-16 10:07:18,905] [INFO] Target genome list was writen to OceanDNA-b4880/target_genomes_gtdb.txt
[2023-03-16 10:07:18,923] [INFO] Task started: fastANI
[2023-03-16 10:07:18,923] [INFO] Running command: fastANI --query /var/lib/cwl/stga850e0d9-4757-4328-908c-f759d5658491/OceanDNA-b4880.fa --refList OceanDNA-b4880/target_genomes_gtdb.txt --output OceanDNA-b4880/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:07:24,454] [INFO] Task succeeded: fastANI
[2023-03-16 10:07:24,462] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:07:24,462] [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_002730985.1	s__BACL11 sp002730985	80.9731	207	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	97.22	97.22	0.84	0.84	2	-
GCA_002693745.1	s__BACL11 sp002693745	77.8238	135	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__BACL11	95.0	98.58	98.58	0.90	0.90	2	-
GCA_905479165.1	s__UWMA-0277 sp905479165	77.1469	107	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002705205.1	s__GCA-2705205 sp002705205	77.0807	87	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2705205	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478765.1	s__UWMA-0277 sp905478765	76.885	122	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711125.1	s__GCA-2711125 sp002711125	76.8101	94	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2711125	95.0	97.93	96.61	0.96	0.94	3	-
GCA_905478185.1	s__UWMA-0277 sp905478185	76.7961	122	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	96.67	96.67	0.88	0.88	2	-
GCA_018664745.1	s__UWMA-0277 sp018664745	76.6126	74	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012960805.1	s__UWMA-0277 sp012960805	76.3892	91	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182255.1	s__UWMA-0277 sp905182255	76.2711	54	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014384505.1	s__UWMA-0277 sp014384505	76.2546	80	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__UWMA-0277	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002728175.1	s__GCA-2697505 sp002728175	76.2116	65	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__GCA-2697505	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181585.1	s__CAJIYG01 sp905181585	75.9882	65	368	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__BACL11;g__CAJIYG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 10:07:24,463] [INFO] GTDB search result was written to OceanDNA-b4880/result_gtdb.tsv
[2023-03-16 10:07:24,463] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:07:24,464] [INFO] DFAST_QC result json was written to OceanDNA-b4880/dqc_result.json
[2023-03-16 10:07:24,464] [INFO] DFAST_QC completed!
[2023-03-16 10:07:24,464] [INFO] Total running time: 0h0m51s