[2023-03-16 19:57:56,492] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:57:56,492] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:57:56,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference
[2023-03-16 19:57:57,584] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:57:57,585] [INFO] Task started: Prodigal
[2023-03-16 19:57:57,585] [INFO] Running command: cat /var/lib/cwl/stge95a8971-95eb-43fa-8d2a-874751830918/OceanDNA-b5526.fa | prodigal -d OceanDNA-b5526/cds.fna -a OceanDNA-b5526/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:58:13,242] [INFO] Task succeeded: Prodigal
[2023-03-16 19:58:13,243] [INFO] Task started: HMMsearch
[2023-03-16 19:58:13,243] [INFO] Running command: hmmsearch --tblout OceanDNA-b5526/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/reference_markers.hmm OceanDNA-b5526/protein.faa > /dev/null
[2023-03-16 19:58:13,414] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:58:13,414] [INFO] Found 6/6 markers.
[2023-03-16 19:58:13,430] [INFO] Query marker FASTA was written to OceanDNA-b5526/markers.fasta
[2023-03-16 19:58:13,431] [INFO] Task started: Blastn
[2023-03-16 19:58:13,431] [INFO] Running command: blastn -query OceanDNA-b5526/markers.fasta -db /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/reference_markers.fasta -out OceanDNA-b5526/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:58:13,955] [INFO] Task succeeded: Blastn
[2023-03-16 19:58:13,956] [INFO] Selected 29 target genomes.
[2023-03-16 19:58:13,956] [INFO] Target genome list was writen to OceanDNA-b5526/target_genomes.txt
[2023-03-16 19:58:13,975] [INFO] Task started: fastANI
[2023-03-16 19:58:13,975] [INFO] Running command: fastANI --query /var/lib/cwl/stge95a8971-95eb-43fa-8d2a-874751830918/OceanDNA-b5526.fa --refList OceanDNA-b5526/target_genomes.txt --output OceanDNA-b5526/fastani_result.tsv --threads 1
[2023-03-16 19:58:29,453] [INFO] Task succeeded: fastANI
[2023-03-16 19:58:29,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:58:29,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:58:29,454] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:58:29,454] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:58:29,454] [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 19:58:29,454] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5526/tc_result.tsv
[2023-03-16 19:58:29,454] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:58:29,454] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:58:29,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/checkm_data
[2023-03-16 19:58:29,457] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:58:29,481] [INFO] Task started: CheckM
[2023-03-16 19:58:29,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5526/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5526/checkm_input OceanDNA-b5526/checkm_result
[2023-03-16 19:59:12,076] [INFO] Task succeeded: CheckM
[2023-03-16 19:59:12,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:59:12,079] [INFO] ===== Completeness check finished =====
[2023-03-16 19:59:12,079] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:59:12,079] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5526/markers.fasta)
[2023-03-16 19:59:12,080] [INFO] Task started: Blastn
[2023-03-16 19:59:12,080] [INFO] Running command: blastn -query OceanDNA-b5526/markers.fasta -db /var/lib/cwl/stg396007a3-a21a-42f4-824f-37d2e2c98ee4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5526/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:59:12,830] [INFO] Task succeeded: Blastn
[2023-03-16 19:59:12,831] [INFO] Selected 18 target genomes.
[2023-03-16 19:59:12,831] [INFO] Target genome list was writen to OceanDNA-b5526/target_genomes_gtdb.txt
[2023-03-16 19:59:12,850] [INFO] Task started: fastANI
[2023-03-16 19:59:12,850] [INFO] Running command: fastANI --query /var/lib/cwl/stge95a8971-95eb-43fa-8d2a-874751830918/OceanDNA-b5526.fa --refList OceanDNA-b5526/target_genomes_gtdb.txt --output OceanDNA-b5526/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:59:20,317] [INFO] Task succeeded: fastANI
[2023-03-16 19:59:20,322] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 19:59:20,323] [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_905480165.1	s__UBA952 sp905480165	98.4493	498	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018665005.1	s__UBA952 sp018665005	93.0597	499	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.77	98.77	0.77	0.77	2	-
GCA_011522905.1	s__UBA952 sp011522905	78.2976	235	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003331365.1	s__UBA952 sp003331365	77.7023	237	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002480215.1	s__UBA952 sp002480215	77.3332	90	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.70	99.70	0.81	0.81	2	-
GCA_905182495.1	s__UBA952 sp905182495	77.2733	107	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002167775.1	s__UBA952 sp002167775	76.9364	107	743	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	98.23	98.23	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2023-03-16 19:59:20,323] [INFO] GTDB search result was written to OceanDNA-b5526/result_gtdb.tsv
[2023-03-16 19:59:20,323] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:59:20,324] [INFO] DFAST_QC result json was written to OceanDNA-b5526/dqc_result.json
[2023-03-16 19:59:20,324] [INFO] DFAST_QC completed!
[2023-03-16 19:59:20,324] [INFO] Total running time: 0h1m24s