[2023-03-17 07:28:31,298] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:28:31,298] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:28:31,298] [INFO] DQC Reference Directory: /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference
[2023-03-17 07:28:33,078] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:28:33,082] [INFO] Task started: Prodigal
[2023-03-17 07:28:33,082] [INFO] Running command: cat /var/lib/cwl/stg10cd40c1-fd1f-497e-b7b1-ab9ceb938f71/OceanDNA-b5728.fa | prodigal -d OceanDNA-b5728/cds.fna -a OceanDNA-b5728/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:28:44,657] [INFO] Task succeeded: Prodigal
[2023-03-17 07:28:44,657] [INFO] Task started: HMMsearch
[2023-03-17 07:28:44,657] [INFO] Running command: hmmsearch --tblout OceanDNA-b5728/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/reference_markers.hmm OceanDNA-b5728/protein.faa > /dev/null
[2023-03-17 07:28:44,843] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:28:44,843] [INFO] Found 6/6 markers.
[2023-03-17 07:28:44,854] [INFO] Query marker FASTA was written to OceanDNA-b5728/markers.fasta
[2023-03-17 07:28:44,854] [INFO] Task started: Blastn
[2023-03-17 07:28:44,854] [INFO] Running command: blastn -query OceanDNA-b5728/markers.fasta -db /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/reference_markers.fasta -out OceanDNA-b5728/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:28:45,425] [INFO] Task succeeded: Blastn
[2023-03-17 07:28:45,426] [INFO] Selected 31 target genomes.
[2023-03-17 07:28:45,426] [INFO] Target genome list was writen to OceanDNA-b5728/target_genomes.txt
[2023-03-17 07:28:45,442] [INFO] Task started: fastANI
[2023-03-17 07:28:45,442] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cd40c1-fd1f-497e-b7b1-ab9ceb938f71/OceanDNA-b5728.fa --refList OceanDNA-b5728/target_genomes.txt --output OceanDNA-b5728/fastani_result.tsv --threads 1
[2023-03-17 07:29:10,821] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:10,822] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:29:10,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:29:10,822] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:29:10,822] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 07:29:10,822] [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
--------------------------------------------------------------------------------
[2023-03-17 07:29:10,822] [INFO] DFAST Taxonomy check result was written to OceanDNA-b5728/tc_result.tsv
[2023-03-17 07:29:10,822] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:29:10,823] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:29:10,823] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/checkm_data
[2023-03-17 07:29:10,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:29:10,828] [INFO] Task started: CheckM
[2023-03-17 07:29:10,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b5728/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b5728/checkm_input OceanDNA-b5728/checkm_result
[2023-03-17 07:29:43,654] [INFO] Task succeeded: CheckM
[2023-03-17 07:29:43,654] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 07:29:43,656] [INFO] ===== Completeness check finished =====
[2023-03-17 07:29:43,656] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:29:43,656] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b5728/markers.fasta)
[2023-03-17 07:29:43,657] [INFO] Task started: Blastn
[2023-03-17 07:29:43,657] [INFO] Running command: blastn -query OceanDNA-b5728/markers.fasta -db /var/lib/cwl/stge8aed086-1639-4f12-8663-a40ad169a6cf/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b5728/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:29:44,369] [INFO] Task succeeded: Blastn
[2023-03-17 07:29:44,370] [INFO] Selected 16 target genomes.
[2023-03-17 07:29:44,370] [INFO] Target genome list was writen to OceanDNA-b5728/target_genomes_gtdb.txt
[2023-03-17 07:29:44,620] [INFO] Task started: fastANI
[2023-03-17 07:29:44,620] [INFO] Running command: fastANI --query /var/lib/cwl/stg10cd40c1-fd1f-497e-b7b1-ab9ceb938f71/OceanDNA-b5728.fa --refList OceanDNA-b5728/target_genomes_gtdb.txt --output OceanDNA-b5728/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:29:50,652] [INFO] Task succeeded: fastANI
[2023-03-17 07:29:50,657] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 07:29:50,657] [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_003451355.1	s__TMED14 sp003451355	99.2235	292	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903821715.1	s__TMED14 sp903821715	90.1191	311	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016868755.1	s__TMED14 sp016868755	82.4301	276	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005786915.1	s__TMED14 sp005786915	82.0773	206	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292855.1	s__TMED14 sp002292855	80.7914	207	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737315.1	s__TMED14 sp002737315	79.5953	180	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	99.85	99.85	0.92	0.92	2	-
GCA_013205365.1	s__TMED14 sp013205365	79.0548	171	381	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__TMED14	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:29:50,658] [INFO] GTDB search result was written to OceanDNA-b5728/result_gtdb.tsv
[2023-03-17 07:29:50,658] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:29:50,659] [INFO] DFAST_QC result json was written to OceanDNA-b5728/dqc_result.json
[2023-03-17 07:29:50,659] [INFO] DFAST_QC completed!
[2023-03-17 07:29:50,659] [INFO] Total running time: 0h1m19s