[2023-03-18 09:41:07,188] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:41:07,188] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:41:07,188] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference
[2023-03-18 09:41:08,294] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:41:08,294] [INFO] Task started: Prodigal
[2023-03-18 09:41:08,294] [INFO] Running command: cat /var/lib/cwl/stgb7668cc4-2949-4913-8240-abdf9dacbe82/OceanDNA-a2194.fa | prodigal -d OceanDNA-a2194/cds.fna -a OceanDNA-a2194/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:41:15,584] [INFO] Task succeeded: Prodigal
[2023-03-18 09:41:15,585] [INFO] Task started: HMMsearch
[2023-03-18 09:41:15,585] [INFO] Running command: hmmsearch --tblout OceanDNA-a2194/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/reference_markers.hmm OceanDNA-a2194/protein.faa > /dev/null
[2023-03-18 09:41:15,754] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:41:15,754] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb7668cc4-2949-4913-8240-abdf9dacbe82/OceanDNA-a2194.fa]
[2023-03-18 09:41:15,765] [INFO] Query marker FASTA was written to OceanDNA-a2194/markers.fasta
[2023-03-18 09:41:15,766] [INFO] Task started: Blastn
[2023-03-18 09:41:15,766] [INFO] Running command: blastn -query OceanDNA-a2194/markers.fasta -db /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/reference_markers.fasta -out OceanDNA-a2194/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:16,193] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:16,193] [INFO] Selected 5 target genomes.
[2023-03-18 09:41:16,194] [INFO] Target genome list was writen to OceanDNA-a2194/target_genomes.txt
[2023-03-18 09:41:16,197] [INFO] Task started: fastANI
[2023-03-18 09:41:16,197] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7668cc4-2949-4913-8240-abdf9dacbe82/OceanDNA-a2194.fa --refList OceanDNA-a2194/target_genomes.txt --output OceanDNA-a2194/fastani_result.tsv --threads 1
[2023-03-18 09:41:18,027] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:18,027] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:41:18,028] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:41:18,028] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:41:18,028] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:41:18,028] [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 09:41:18,028] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2194/tc_result.tsv
[2023-03-18 09:41:18,028] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:41:18,028] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:41:18,028] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/checkm_data
[2023-03-18 09:41:18,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:41:18,034] [INFO] Task started: CheckM
[2023-03-18 09:41:18,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2194/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2194/checkm_input OceanDNA-a2194/checkm_result
[2023-03-18 09:41:41,866] [INFO] Task succeeded: CheckM
[2023-03-18 09:41:41,867] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.05%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:41:41,869] [INFO] ===== Completeness check finished =====
[2023-03-18 09:41:41,869] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:41:41,869] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2194/markers.fasta)
[2023-03-18 09:41:41,869] [INFO] Task started: Blastn
[2023-03-18 09:41:41,869] [INFO] Running command: blastn -query OceanDNA-a2194/markers.fasta -db /var/lib/cwl/stgbf127740-5a31-4249-ac42-ca57b273392a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2194/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:41:42,312] [INFO] Task succeeded: Blastn
[2023-03-18 09:41:42,313] [INFO] Selected 9 target genomes.
[2023-03-18 09:41:42,313] [INFO] Target genome list was writen to OceanDNA-a2194/target_genomes_gtdb.txt
[2023-03-18 09:41:42,322] [INFO] Task started: fastANI
[2023-03-18 09:41:42,322] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7668cc4-2949-4913-8240-abdf9dacbe82/OceanDNA-a2194.fa --refList OceanDNA-a2194/target_genomes_gtdb.txt --output OceanDNA-a2194/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:41:45,283] [INFO] Task succeeded: fastANI
[2023-03-18 09:41:45,289] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 09:41:45,289] [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_011526375.1	s__MGIIa-L1 sp011526375	82.8077	368	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013329295.1	s__MGIIa-L1 sp9596u	78.708	218	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	99.26	0.88	0.84	4	-
GCA_002506025.1	s__MGIIa-L1 sp002506025	77.2668	96	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009887195.1	s__MGIIa-L1 sp009887195	77.0657	125	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.91	98.88	0.90	0.86	3	-
GCA_002726395.1	s__MGIIa-L1 sp002726395	76.8702	117	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.39	99.39	0.85	0.85	2	-
GCA_018659375.1	s__MGIIa-L1 sp018659375	76.7477	132	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.93	0.93	2	-
GCA_002702945.1	s__MGIIa-L1 sp002702945	76.6843	84	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	98.55	98.53	0.86	0.86	3	-
GCA_003602575.1	s__MGIIa-L1 sp003602575	76.3836	78	439	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:41:45,290] [INFO] GTDB search result was written to OceanDNA-a2194/result_gtdb.tsv
[2023-03-18 09:41:45,290] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:41:45,290] [INFO] DFAST_QC result json was written to OceanDNA-a2194/dqc_result.json
[2023-03-18 09:41:45,291] [INFO] DFAST_QC completed!
[2023-03-18 09:41:45,291] [INFO] Total running time: 0h0m38s