[2023-03-16 21:45:13,526] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,526] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,526] [INFO] DQC Reference Directory: /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference
[2023-03-16 21:45:15,325] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:15,327] [INFO] Task started: Prodigal
[2023-03-16 21:45:15,327] [INFO] Running command: cat /var/lib/cwl/stgee162a4e-c52f-45a8-b675-ca3b74a324e4/OceanDNA-b14422.fa | prodigal -d OceanDNA-b14422/cds.fna -a OceanDNA-b14422/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:26,892] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:26,892] [INFO] Task started: HMMsearch
[2023-03-16 21:45:26,892] [INFO] Running command: hmmsearch --tblout OceanDNA-b14422/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/reference_markers.hmm OceanDNA-b14422/protein.faa > /dev/null
[2023-03-16 21:45:27,076] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:27,077] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgee162a4e-c52f-45a8-b675-ca3b74a324e4/OceanDNA-b14422.fa]
[2023-03-16 21:45:27,091] [INFO] Query marker FASTA was written to OceanDNA-b14422/markers.fasta
[2023-03-16 21:45:27,092] [INFO] Task started: Blastn
[2023-03-16 21:45:27,092] [INFO] Running command: blastn -query OceanDNA-b14422/markers.fasta -db /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/reference_markers.fasta -out OceanDNA-b14422/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:27,623] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:27,624] [INFO] Selected 17 target genomes.
[2023-03-16 21:45:27,624] [INFO] Target genome list was writen to OceanDNA-b14422/target_genomes.txt
[2023-03-16 21:45:27,633] [INFO] Task started: fastANI
[2023-03-16 21:45:27,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgee162a4e-c52f-45a8-b675-ca3b74a324e4/OceanDNA-b14422.fa --refList OceanDNA-b14422/target_genomes.txt --output OceanDNA-b14422/fastani_result.tsv --threads 1
[2023-03-16 21:45:37,816] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:37,816] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:37,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:37,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 21:45:37,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 21:45:37,817] [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 21:45:37,817] [INFO] DFAST Taxonomy check result was written to OceanDNA-b14422/tc_result.tsv
[2023-03-16 21:45:37,817] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:37,817] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:37,818] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/checkm_data
[2023-03-16 21:45:37,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:37,824] [INFO] Task started: CheckM
[2023-03-16 21:45:37,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b14422/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b14422/checkm_input OceanDNA-b14422/checkm_result
[2023-03-16 21:46:10,622] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:10,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:10,625] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:10,625] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:10,625] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b14422/markers.fasta)
[2023-03-16 21:46:10,626] [INFO] Task started: Blastn
[2023-03-16 21:46:10,626] [INFO] Running command: blastn -query OceanDNA-b14422/markers.fasta -db /var/lib/cwl/stg0238aa77-af22-4982-8fee-afddefd7b57b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b14422/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:11,337] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:11,338] [INFO] Selected 16 target genomes.
[2023-03-16 21:46:11,338] [INFO] Target genome list was writen to OceanDNA-b14422/target_genomes_gtdb.txt
[2023-03-16 21:46:11,374] [INFO] Task started: fastANI
[2023-03-16 21:46:11,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgee162a4e-c52f-45a8-b675-ca3b74a324e4/OceanDNA-b14422.fa --refList OceanDNA-b14422/target_genomes_gtdb.txt --output OceanDNA-b14422/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:46:18,274] [INFO] Task succeeded: fastANI
[2023-03-16 21:46:18,278] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 21:46:18,279] [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_012959765.1	s__UBA1328 sp012959765	78.4448	264	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_018650845.1	s__UBA1328 sp018650845	78.0628	178	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	-
GCA_002501045.1	s__UBA1328 sp002501045	77.9999	146	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
GCA_018673955.1	s__UBA1328 sp018673955	77.5548	141	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
GCA_018649665.1	s__UBA1328 sp018649665	77.5301	155	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002306815.1	s__UBA1328 sp002306815	76.8071	98	648	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	98.45	96.89	0.85	0.79	5	-
--------------------------------------------------------------------------------
[2023-03-16 21:46:18,279] [INFO] GTDB search result was written to OceanDNA-b14422/result_gtdb.tsv
[2023-03-16 21:46:18,279] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:46:18,280] [INFO] DFAST_QC result json was written to OceanDNA-b14422/dqc_result.json
[2023-03-16 21:46:18,280] [INFO] DFAST_QC completed!
[2023-03-16 21:46:18,280] [INFO] Total running time: 0h1m5s