[2023-03-16 17:22:04,290] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:22:04,290] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:22:04,290] [INFO] DQC Reference Directory: /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference
[2023-03-16 17:22:06,060] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:22:06,061] [INFO] Task started: Prodigal
[2023-03-16 17:22:06,061] [INFO] Running command: cat /var/lib/cwl/stg88a6eb48-06d6-44fa-b721-19eb572b6557/OceanDNA-b5747.fa | prodigal -d OceanDNA-b5747/cds.fna -a OceanDNA-b5747/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:22:16,927] [INFO] Task succeeded: Prodigal
[2023-03-16 17:22:16,927] [INFO] Task started: HMMsearch
[2023-03-16 17:22:16,927] [INFO] Running command: hmmsearch --tblout OceanDNA-b5747/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/reference_markers.hmm OceanDNA-b5747/protein.faa > /dev/null
[2023-03-16 17:22:17,135] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:22:17,136] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88a6eb48-06d6-44fa-b721-19eb572b6557/OceanDNA-b5747.fa]
[2023-03-16 17:22:17,149] [INFO] Query marker FASTA was written to OceanDNA-b5747/markers.fasta
[2023-03-16 17:22:17,150] [INFO] Task started: Blastn
[2023-03-16 17:22:17,150] [INFO] Running command: blastn -query OceanDNA-b5747/markers.fasta -db /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/reference_markers.fasta -out OceanDNA-b5747/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:22:20,318] [INFO] Task succeeded: Blastn
[2023-03-16 17:22:20,319] [INFO] Selected 27 target genomes.
[2023-03-16 17:22:20,319] [INFO] Target genome list was writen to OceanDNA-b5747/target_genomes.txt
[2023-03-16 17:22:20,337] [INFO] Task started: fastANI
[2023-03-16 17:22:20,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a6eb48-06d6-44fa-b721-19eb572b6557/OceanDNA-b5747.fa --refList OceanDNA-b5747/target_genomes.txt --output OceanDNA-b5747/fastani_result.tsv --threads 1
[2023-03-16 17:22:35,307] [INFO] Task succeeded: fastANI
[2023-03-16 17:22:35,308] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:22:35,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:22:35,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:22:35,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 17:22:35,308] [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 17:22:35,308] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5747/tc_result.tsv
[2023-03-16 17:22:35,308] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:22:35,308] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:22:35,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/checkm_data
[2023-03-16 17:22:35,311] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:22:35,315] [INFO] Task started: CheckM
[2023-03-16 17:22:35,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5747/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5747/checkm_input OceanDNA-b5747/checkm_result
[2023-03-16 17:23:20,482] [INFO] Task succeeded: CheckM
[2023-03-16 17:23:20,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:23:20,485] [INFO] ===== Completeness check finished =====
[2023-03-16 17:23:20,485] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:23:20,485] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5747/markers.fasta)
[2023-03-16 17:23:20,487] [INFO] Task started: Blastn
[2023-03-16 17:23:20,487] [INFO] Running command: blastn -query OceanDNA-b5747/markers.fasta -db /var/lib/cwl/stgf690d788-e14c-426c-8a63-031dc730e18b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5747/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:23:21,865] [INFO] Task succeeded: Blastn
[2023-03-16 17:23:21,866] [INFO] Selected 15 target genomes.
[2023-03-16 17:23:21,867] [INFO] Target genome list was writen to OceanDNA-b5747/target_genomes_gtdb.txt
[2023-03-16 17:23:21,892] [INFO] Task started: fastANI
[2023-03-16 17:23:21,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a6eb48-06d6-44fa-b721-19eb572b6557/OceanDNA-b5747.fa --refList OceanDNA-b5747/target_genomes_gtdb.txt --output OceanDNA-b5747/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:23:28,191] [INFO] Task succeeded: fastANI
[2023-03-16 17:23:28,197] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:23:28,197] [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_018402665.1	s__UBA10364 sp018402665	96.4719	373	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	conclusive
GCA_905478295.1	s__UBA10364 sp002387615	86.2299	343	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_003045825.1	s__UBA10364 sp003045825	84.5132	312	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	-
GCA_002685435.1	s__UBA10364 sp002685435	84.3244	265	397	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	78.5413	105	397	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	78.4503	107	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_003455605.1	s__UBA10364 sp003455605	78.0087	55	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002707525.1	s__UBA10364 sp002707525	77.0145	56	397	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:23:28,198] [INFO] GTDB search result was written to OceanDNA-b5747/result_gtdb.tsv
[2023-03-16 17:23:28,198] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:23:28,199] [INFO] DFAST_QC result json was written to OceanDNA-b5747/dqc_result.json
[2023-03-16 17:23:28,200] [INFO] DFAST_QC completed!
[2023-03-16 17:23:28,200] [INFO] Total running time: 0h1m24s