[2023-03-18 23:31:26,241] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:31:26,241] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:31:26,241] [INFO] DQC Reference Directory: /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference
[2023-03-18 23:31:27,323] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:31:27,323] [INFO] Task started: Prodigal
[2023-03-18 23:31:27,323] [INFO] Running command: cat /var/lib/cwl/stg29040bae-3888-4003-a2ca-1fc9a84ed46a/OceanDNA-a2559.fa | prodigal -d OceanDNA-a2559/cds.fna -a OceanDNA-a2559/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:31:39,107] [INFO] Task succeeded: Prodigal
[2023-03-18 23:31:39,107] [INFO] Task started: HMMsearch
[2023-03-18 23:31:39,107] [INFO] Running command: hmmsearch --tblout OceanDNA-a2559/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/reference_markers.hmm OceanDNA-a2559/protein.faa > /dev/null
[2023-03-18 23:31:39,275] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:31:39,275] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg29040bae-3888-4003-a2ca-1fc9a84ed46a/OceanDNA-a2559.fa]
[2023-03-18 23:31:39,289] [INFO] Query marker FASTA was written to OceanDNA-a2559/markers.fasta
[2023-03-18 23:31:39,290] [INFO] Task started: Blastn
[2023-03-18 23:31:39,290] [INFO] Running command: blastn -query OceanDNA-a2559/markers.fasta -db /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/reference_markers.fasta -out OceanDNA-a2559/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:31:39,718] [INFO] Task succeeded: Blastn
[2023-03-18 23:31:39,719] [INFO] Selected 4 target genomes.
[2023-03-18 23:31:39,719] [INFO] Target genome list was writen to OceanDNA-a2559/target_genomes.txt
[2023-03-18 23:31:39,722] [INFO] Task started: fastANI
[2023-03-18 23:31:39,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg29040bae-3888-4003-a2ca-1fc9a84ed46a/OceanDNA-a2559.fa --refList OceanDNA-a2559/target_genomes.txt --output OceanDNA-a2559/fastani_result.tsv --threads 1
[2023-03-18 23:31:41,283] [INFO] Task succeeded: fastANI
[2023-03-18 23:31:41,283] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:31:41,283] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:31:41,283] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:31:41,283] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:31:41,283] [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 23:31:41,284] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2559/tc_result.tsv
[2023-03-18 23:31:41,284] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:31:41,284] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:31:41,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/checkm_data
[2023-03-18 23:31:41,286] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:31:41,315] [INFO] Task started: CheckM
[2023-03-18 23:31:41,315] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2559/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2559/checkm_input OceanDNA-a2559/checkm_result
[2023-03-18 23:32:15,604] [INFO] Task succeeded: CheckM
[2023-03-18 23:32:15,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.11%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:32:15,607] [INFO] ===== Completeness check finished =====
[2023-03-18 23:32:15,607] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:32:15,607] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2559/markers.fasta)
[2023-03-18 23:32:15,608] [INFO] Task started: Blastn
[2023-03-18 23:32:15,608] [INFO] Running command: blastn -query OceanDNA-a2559/markers.fasta -db /var/lib/cwl/stga3980521-f08c-49e6-916f-6ccb874641af/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2559/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:32:16,011] [INFO] Task succeeded: Blastn
[2023-03-18 23:32:16,011] [INFO] Selected 9 target genomes.
[2023-03-18 23:32:16,011] [INFO] Target genome list was writen to OceanDNA-a2559/target_genomes_gtdb.txt
[2023-03-18 23:32:16,018] [INFO] Task started: fastANI
[2023-03-18 23:32:16,018] [INFO] Running command: fastANI --query /var/lib/cwl/stg29040bae-3888-4003-a2ca-1fc9a84ed46a/OceanDNA-a2559.fa --refList OceanDNA-a2559/target_genomes_gtdb.txt --output OceanDNA-a2559/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:32:18,796] [INFO] Task succeeded: fastANI
[2023-03-18 23:32:18,800] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:32:18,800] [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_002499545.1	s__MGIIa-L1 sp002499545	99.8366	540	610	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.68	99.68	0.84	0.84	2	conclusive
GCA_002499705.1	s__MGIIa-L1 sp002499705	77.3563	149	610	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_002506275.1	s__MGIIa-L1 sp002506275	77.2492	82	610	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.51	98.77	0.87	0.72	5	-
GCA_018701175.1	s__MGIIa-L1 sp018701175	77.2343	145	610	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.50	99.46	0.87	0.84	5	-
GCA_018662825.1	s__MGIIa-L1 sp018662825	77.1371	139	610	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_905182635.1	s__MGIIa-L1 sp905182635	76.8312	90	610	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 23:32:18,801] [INFO] GTDB search result was written to OceanDNA-a2559/result_gtdb.tsv
[2023-03-18 23:32:18,801] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:32:18,802] [INFO] DFAST_QC result json was written to OceanDNA-a2559/dqc_result.json
[2023-03-18 23:32:18,802] [INFO] DFAST_QC completed!
[2023-03-18 23:32:18,802] [INFO] Total running time: 0h0m53s