[2023-03-15 20:34:26,716] [INFO] DFAST_QC pipeline started.
[2023-03-15 20:34:26,716] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 20:34:26,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference
[2023-03-15 20:34:28,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 20:34:28,458] [INFO] Task started: Prodigal
[2023-03-15 20:34:28,458] [INFO] Running command: cat /var/lib/cwl/stg18ba16e1-add7-4d10-87b1-01c4603599e9/OceanDNA-b12362.fa | prodigal -d OceanDNA-b12362/cds.fna -a OceanDNA-b12362/protein.faa -g 11 -q > /dev/null
[2023-03-15 20:34:39,112] [INFO] Task succeeded: Prodigal
[2023-03-15 20:34:39,113] [INFO] Task started: HMMsearch
[2023-03-15 20:34:39,113] [INFO] Running command: hmmsearch --tblout OceanDNA-b12362/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/reference_markers.hmm OceanDNA-b12362/protein.faa > /dev/null
[2023-03-15 20:34:39,303] [INFO] Task succeeded: HMMsearch
[2023-03-15 20:34:39,303] [INFO] Found 6/6 markers.
[2023-03-15 20:34:39,317] [INFO] Query marker FASTA was written to OceanDNA-b12362/markers.fasta
[2023-03-15 20:34:39,317] [INFO] Task started: Blastn
[2023-03-15 20:34:39,317] [INFO] Running command: blastn -query OceanDNA-b12362/markers.fasta -db /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/reference_markers.fasta -out OceanDNA-b12362/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:34:39,832] [INFO] Task succeeded: Blastn
[2023-03-15 20:34:39,833] [INFO] Selected 23 target genomes.
[2023-03-15 20:34:39,833] [INFO] Target genome list was writen to OceanDNA-b12362/target_genomes.txt
[2023-03-15 20:34:39,847] [INFO] Task started: fastANI
[2023-03-15 20:34:39,847] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ba16e1-add7-4d10-87b1-01c4603599e9/OceanDNA-b12362.fa --refList OceanDNA-b12362/target_genomes.txt --output OceanDNA-b12362/fastani_result.tsv --threads 1
[2023-03-15 20:34:52,433] [INFO] Task succeeded: fastANI
[2023-03-15 20:34:52,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 20:34:52,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 20:34:52,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 20:34:52,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 20:34:52,434] [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
--------------------------------------------------------------------------------
[2023-03-15 20:34:52,434] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12362/tc_result.tsv
[2023-03-15 20:34:52,434] [INFO] ===== Taxonomy check completed =====
[2023-03-15 20:34:52,435] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 20:34:52,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/checkm_data
[2023-03-15 20:34:52,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 20:34:52,441] [INFO] Task started: CheckM
[2023-03-15 20:34:52,441] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12362/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12362/checkm_input OceanDNA-b12362/checkm_result
[2023-03-15 20:35:22,966] [INFO] Task succeeded: CheckM
[2023-03-15 20:35:22,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 20:35:22,968] [INFO] ===== Completeness check finished =====
[2023-03-15 20:35:22,968] [INFO] ===== Start GTDB Search =====
[2023-03-15 20:35:22,969] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12362/markers.fasta)
[2023-03-15 20:35:22,969] [INFO] Task started: Blastn
[2023-03-15 20:35:22,969] [INFO] Running command: blastn -query OceanDNA-b12362/markers.fasta -db /var/lib/cwl/stg4ce067d9-08a5-4f82-b0a4-188333ced1f2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12362/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 20:35:23,688] [INFO] Task succeeded: Blastn
[2023-03-15 20:35:23,689] [INFO] Selected 11 target genomes.
[2023-03-15 20:35:23,689] [INFO] Target genome list was writen to OceanDNA-b12362/target_genomes_gtdb.txt
[2023-03-15 20:35:23,856] [INFO] Task started: fastANI
[2023-03-15 20:35:23,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg18ba16e1-add7-4d10-87b1-01c4603599e9/OceanDNA-b12362.fa --refList OceanDNA-b12362/target_genomes_gtdb.txt --output OceanDNA-b12362/fastani_result_gtdb.tsv --threads 1
[2023-03-15 20:35:28,246] [INFO] Task succeeded: fastANI
[2023-03-15 20:35:28,252] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 20:35:28,252] [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_905182745.1	s__MED-G20 sp905182745	87.9796	277	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780365.1	s__MED-G20 sp016780365	87.0124	409	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_002713405.1	s__MED-G20 sp002713405	87.0028	424	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181675.1	s__MED-G20 sp905181675	83.8714	357	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182525.1	s__MED-G20 sp905182525	79.643	282	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002691605.1	s__MED-G20 sp002691605	77.3965	181	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_002686655.1	s__MED-G20 sp002686655	77.3909	238	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002457645.1	s__MED-G20 sp002457645	77.2912	144	588	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 20:35:28,252] [INFO] GTDB search result was written to OceanDNA-b12362/result_gtdb.tsv
[2023-03-15 20:35:28,252] [INFO] ===== GTDB Search completed =====
[2023-03-15 20:35:28,253] [INFO] DFAST_QC result json was written to OceanDNA-b12362/dqc_result.json
[2023-03-15 20:35:28,253] [INFO] DFAST_QC completed!
[2023-03-15 20:35:28,253] [INFO] Total running time: 0h1m2s