[2023-03-18 00:22:36,357] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:22:36,357] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:22:36,357] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference
[2023-03-18 00:22:38,781] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:22:38,782] [INFO] Task started: Prodigal
[2023-03-18 00:22:38,782] [INFO] Running command: cat /var/lib/cwl/stgcd829e59-b0f4-4b07-b15e-76d06774ef90/OceanDNA-b1142.fa | prodigal -d OceanDNA-b1142/cds.fna -a OceanDNA-b1142/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:51,611] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:51,611] [INFO] Task started: HMMsearch
[2023-03-18 00:22:51,611] [INFO] Running command: hmmsearch --tblout OceanDNA-b1142/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/reference_markers.hmm OceanDNA-b1142/protein.faa > /dev/null
[2023-03-18 00:22:51,776] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:51,776] [INFO] Found 6/6 markers.
[2023-03-18 00:22:51,791] [INFO] Query marker FASTA was written to OceanDNA-b1142/markers.fasta
[2023-03-18 00:22:51,792] [INFO] Task started: Blastn
[2023-03-18 00:22:51,792] [INFO] Running command: blastn -query OceanDNA-b1142/markers.fasta -db /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/reference_markers.fasta -out OceanDNA-b1142/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:52,314] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:52,315] [INFO] Selected 21 target genomes.
[2023-03-18 00:22:52,315] [INFO] Target genome list was writen to OceanDNA-b1142/target_genomes.txt
[2023-03-18 00:22:52,327] [INFO] Task started: fastANI
[2023-03-18 00:22:52,327] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd829e59-b0f4-4b07-b15e-76d06774ef90/OceanDNA-b1142.fa --refList OceanDNA-b1142/target_genomes.txt --output OceanDNA-b1142/fastani_result.tsv --threads 1
[2023-03-18 00:23:06,351] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:06,351] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:23:06,352] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:23:06,352] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:23:06,352] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:23:06,352] [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
--------------------------------------------------------------------------------
[2023-03-18 00:23:06,352] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1142/tc_result.tsv
[2023-03-18 00:23:06,352] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:23:06,353] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:23:06,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/checkm_data
[2023-03-18 00:23:06,356] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:23:06,657] [INFO] Task started: CheckM
[2023-03-18 00:23:06,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1142/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1142/checkm_input OceanDNA-b1142/checkm_result
[2023-03-18 00:23:41,289] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:41,289] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:41,297] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:41,297] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:41,298] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1142/markers.fasta)
[2023-03-18 00:23:41,298] [INFO] Task started: Blastn
[2023-03-18 00:23:41,298] [INFO] Running command: blastn -query OceanDNA-b1142/markers.fasta -db /var/lib/cwl/stgc4bad891-6c32-4314-8f60-01aadba079b7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1142/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:42,013] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:42,015] [INFO] Selected 19 target genomes.
[2023-03-18 00:23:42,015] [INFO] Target genome list was writen to OceanDNA-b1142/target_genomes_gtdb.txt
[2023-03-18 00:23:42,053] [INFO] Task started: fastANI
[2023-03-18 00:23:42,053] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd829e59-b0f4-4b07-b15e-76d06774ef90/OceanDNA-b1142.fa --refList OceanDNA-b1142/target_genomes_gtdb.txt --output OceanDNA-b1142/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:49,173] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:49,179] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:49,179] [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_014237715.1	s__UBA9410 sp014237715	77.5681	198	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_014239855.1	s__UBA9410 sp014239855	77.5608	195	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003541675.1	s__UBA9410 sp003541675	77.4709	122	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845305.1	s__UBA9410 sp016845305	77.3622	165	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714485.1	s__UBA9410 sp002714485	77.0571	130	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961035.1	s__UBA9410 sp012961035	76.8191	106	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_002727895.1	s__UBA9410 sp002727895	76.8029	109	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014240365.1	s__UBA9410 sp014240365	76.6457	90	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_002329075.1	s__S20-B6 sp002329075	76.2401	59	684	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.53	97.43	0.90	0.85	7	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:49,180] [INFO] GTDB search result was written to OceanDNA-b1142/result_gtdb.tsv
[2023-03-18 00:23:49,183] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:49,186] [INFO] DFAST_QC result json was written to OceanDNA-b1142/dqc_result.json
[2023-03-18 00:23:49,186] [INFO] DFAST_QC completed!
[2023-03-18 00:23:49,186] [INFO] Total running time: 0h1m13s