[2023-03-17 02:31:12,705] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,706] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference
[2023-03-17 02:31:13,850] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:13,850] [INFO] Task started: Prodigal
[2023-03-17 02:31:13,850] [INFO] Running command: cat /var/lib/cwl/stg407aafe4-6d0d-4719-8d65-ac7e51ae3fd1/OceanDNA-b6902.fa | prodigal -d OceanDNA-b6902/cds.fna -a OceanDNA-b6902/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:22,529] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:22,529] [INFO] Task started: HMMsearch
[2023-03-17 02:31:22,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b6902/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/reference_markers.hmm OceanDNA-b6902/protein.faa > /dev/null
[2023-03-17 02:31:22,679] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:22,680] [INFO] Found 6/6 markers.
[2023-03-17 02:31:22,691] [INFO] Query marker FASTA was written to OceanDNA-b6902/markers.fasta
[2023-03-17 02:31:22,692] [INFO] Task started: Blastn
[2023-03-17 02:31:22,692] [INFO] Running command: blastn -query OceanDNA-b6902/markers.fasta -db /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/reference_markers.fasta -out OceanDNA-b6902/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:23,203] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:23,203] [INFO] Selected 26 target genomes.
[2023-03-17 02:31:23,204] [INFO] Target genome list was writen to OceanDNA-b6902/target_genomes.txt
[2023-03-17 02:31:23,217] [INFO] Task started: fastANI
[2023-03-17 02:31:23,218] [INFO] Running command: fastANI --query /var/lib/cwl/stg407aafe4-6d0d-4719-8d65-ac7e51ae3fd1/OceanDNA-b6902.fa --refList OceanDNA-b6902/target_genomes.txt --output OceanDNA-b6902/fastani_result.tsv --threads 1
[2023-03-17 02:31:37,117] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:37,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:37,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:37,118] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:37,118] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:31:37,118] [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 02:31:37,118] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6902/tc_result.tsv
[2023-03-17 02:31:37,119] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:37,119] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:37,119] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/checkm_data
[2023-03-17 02:31:37,121] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:37,124] [INFO] Task started: CheckM
[2023-03-17 02:31:37,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6902/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6902/checkm_input OceanDNA-b6902/checkm_result
[2023-03-17 02:32:03,405] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:03,405] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:32:03,407] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:03,407] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:03,407] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6902/markers.fasta)
[2023-03-17 02:32:03,408] [INFO] Task started: Blastn
[2023-03-17 02:32:03,408] [INFO] Running command: blastn -query OceanDNA-b6902/markers.fasta -db /var/lib/cwl/stg97b5d55d-6a75-444b-bd80-aa622fe48181/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6902/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:04,140] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:04,141] [INFO] Selected 21 target genomes.
[2023-03-17 02:32:04,141] [INFO] Target genome list was writen to OceanDNA-b6902/target_genomes_gtdb.txt
[2023-03-17 02:32:04,639] [INFO] Task started: fastANI
[2023-03-17 02:32:04,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg407aafe4-6d0d-4719-8d65-ac7e51ae3fd1/OceanDNA-b6902.fa --refList OceanDNA-b6902/target_genomes_gtdb.txt --output OceanDNA-b6902/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:11,969] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:11,975] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:32:11,976] [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_002711185.1	s__GCA-002723295 sp002711185	97.3217	406	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	98.54	98.54	0.83	0.83	2	conclusive
GCA_002713495.1	s__GCA-002723295 sp002713495	83.0541	371	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721275.1	s__GCA-002723295 sp002721275	80.4797	302	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690805.1	s__GCA-002723295 sp002690805	76.9626	136	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	97.07	97.07	0.76	0.76	2	-
GCA_905182735.1	s__GCA-002723295 sp905182735	76.6931	167	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-002723295	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902560065.1	s__GCA-2719315 sp902560065	76.159	60	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__GCA-2719315	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	75.9198	52	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	75.5863	55	476	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_905381055.1	s__TMED220 sp905381055	75.5054	67	476	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__TMED220	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:11,976] [INFO] GTDB search result was written to OceanDNA-b6902/result_gtdb.tsv
[2023-03-17 02:32:11,976] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:11,977] [INFO] DFAST_QC result json was written to OceanDNA-b6902/dqc_result.json
[2023-03-17 02:32:11,977] [INFO] DFAST_QC completed!
[2023-03-17 02:32:11,977] [INFO] Total running time: 0h0m59s