[2023-03-16 06:31:19,176] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:31:19,177] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:31:19,177] [INFO] DQC Reference Directory: /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference
[2023-03-16 06:31:20,277] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:31:20,277] [INFO] Task started: Prodigal
[2023-03-16 06:31:20,277] [INFO] Running command: cat /var/lib/cwl/stg7a0e6e39-4086-4a53-9563-1dc95f0ff73b/OceanDNA-b5763.fa | prodigal -d OceanDNA-b5763/cds.fna -a OceanDNA-b5763/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:31:33,355] [INFO] Task succeeded: Prodigal
[2023-03-16 06:31:33,355] [INFO] Task started: HMMsearch
[2023-03-16 06:31:33,355] [INFO] Running command: hmmsearch --tblout OceanDNA-b5763/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/reference_markers.hmm OceanDNA-b5763/protein.faa > /dev/null
[2023-03-16 06:31:33,523] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:31:33,523] [INFO] Found 6/6 markers.
[2023-03-16 06:31:33,646] [INFO] Query marker FASTA was written to OceanDNA-b5763/markers.fasta
[2023-03-16 06:31:33,647] [INFO] Task started: Blastn
[2023-03-16 06:31:33,647] [INFO] Running command: blastn -query OceanDNA-b5763/markers.fasta -db /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/reference_markers.fasta -out OceanDNA-b5763/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:31:34,194] [INFO] Task succeeded: Blastn
[2023-03-16 06:31:34,232] [INFO] Selected 25 target genomes.
[2023-03-16 06:31:34,232] [INFO] Target genome list was writen to OceanDNA-b5763/target_genomes.txt
[2023-03-16 06:31:34,249] [INFO] Task started: fastANI
[2023-03-16 06:31:34,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a0e6e39-4086-4a53-9563-1dc95f0ff73b/OceanDNA-b5763.fa --refList OceanDNA-b5763/target_genomes.txt --output OceanDNA-b5763/fastani_result.tsv --threads 1
[2023-03-16 06:31:49,021] [INFO] Task succeeded: fastANI
[2023-03-16 06:31:49,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:31:49,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:31:49,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:31:49,021] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:31:49,021] [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 06:31:49,030] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5763/tc_result.tsv
[2023-03-16 06:31:49,048] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:31:49,048] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:31:49,048] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/checkm_data
[2023-03-16 06:31:49,050] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:31:49,054] [INFO] Task started: CheckM
[2023-03-16 06:31:49,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5763/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5763/checkm_input OceanDNA-b5763/checkm_result
[2023-03-16 06:32:25,756] [INFO] Task succeeded: CheckM
[2023-03-16 06:32:25,756] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:32:25,783] [INFO] ===== Completeness check finished =====
[2023-03-16 06:32:25,783] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:32:25,783] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5763/markers.fasta)
[2023-03-16 06:32:25,784] [INFO] Task started: Blastn
[2023-03-16 06:32:25,784] [INFO] Running command: blastn -query OceanDNA-b5763/markers.fasta -db /var/lib/cwl/stgad570917-5932-41c3-84a5-1b9ae0148bad/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5763/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:32:26,550] [INFO] Task succeeded: Blastn
[2023-03-16 06:32:26,553] [INFO] Selected 16 target genomes.
[2023-03-16 06:32:26,553] [INFO] Target genome list was writen to OceanDNA-b5763/target_genomes_gtdb.txt
[2023-03-16 06:32:26,568] [INFO] Task started: fastANI
[2023-03-16 06:32:26,568] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a0e6e39-4086-4a53-9563-1dc95f0ff73b/OceanDNA-b5763.fa --refList OceanDNA-b5763/target_genomes_gtdb.txt --output OceanDNA-b5763/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:32:32,521] [INFO] Task succeeded: fastANI
[2023-03-16 06:32:32,528] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:32:32,528] [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_002378005.1	s__UBA10364 sp002378005	89.787	422	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.86	99.85	0.95	0.94	3	-
GCA_003445735.1	s__UBA10364 sp003445735	87.3377	313	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_003455605.1	s__UBA10364 sp003455605	86.1834	245	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002430755.1	s__UBA10364 sp002430755	79.7529	88	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012269745.1	s__UBA10364 sp012269745	79.384	139	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525035.1	s__UBA10364 sp011525035	79.1412	155	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003385605.1	s__UBA10364 sp003385605	78.9885	153	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_013911625.1	s__UBA10364 sp013911625	78.8298	70	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623275.1	s__UBA10364 sp018623275	78.4979	98	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905478295.1	s__UBA10364 sp002387615	77.8345	118	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_018402665.1	s__UBA10364 sp018402665	77.807	150	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:32:32,530] [INFO] GTDB search result was written to OceanDNA-b5763/result_gtdb.tsv
[2023-03-16 06:32:32,530] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:32:32,531] [INFO] DFAST_QC result json was written to OceanDNA-b5763/dqc_result.json
[2023-03-16 06:32:32,531] [INFO] DFAST_QC completed!
[2023-03-16 06:32:32,531] [INFO] Total running time: 0h1m13s