[2023-03-19 04:11:06,928] [INFO] DFAST_QC pipeline started.
[2023-03-19 04:11:06,928] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 04:11:06,928] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference
[2023-03-19 04:11:08,640] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 04:11:08,641] [INFO] Task started: Prodigal
[2023-03-19 04:11:08,641] [INFO] Running command: cat /var/lib/cwl/stga0b679ea-9fc3-4dec-b444-546fd9574bbd/OceanDNA-b3556.fa | prodigal -d OceanDNA-b3556/cds.fna -a OceanDNA-b3556/protein.faa -g 11 -q > /dev/null
[2023-03-19 04:11:34,067] [INFO] Task succeeded: Prodigal
[2023-03-19 04:11:34,068] [INFO] Task started: HMMsearch
[2023-03-19 04:11:34,068] [INFO] Running command: hmmsearch --tblout OceanDNA-b3556/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/reference_markers.hmm OceanDNA-b3556/protein.faa > /dev/null
[2023-03-19 04:11:34,292] [INFO] Task succeeded: HMMsearch
[2023-03-19 04:11:34,293] [INFO] Found 6/6 markers.
[2023-03-19 04:11:34,323] [INFO] Query marker FASTA was written to OceanDNA-b3556/markers.fasta
[2023-03-19 04:11:34,323] [INFO] Task started: Blastn
[2023-03-19 04:11:34,323] [INFO] Running command: blastn -query OceanDNA-b3556/markers.fasta -db /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/reference_markers.fasta -out OceanDNA-b3556/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:11:34,841] [INFO] Task succeeded: Blastn
[2023-03-19 04:11:34,842] [INFO] Selected 25 target genomes.
[2023-03-19 04:11:34,842] [INFO] Target genome list was writen to OceanDNA-b3556/target_genomes.txt
[2023-03-19 04:11:34,856] [INFO] Task started: fastANI
[2023-03-19 04:11:34,856] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b679ea-9fc3-4dec-b444-546fd9574bbd/OceanDNA-b3556.fa --refList OceanDNA-b3556/target_genomes.txt --output OceanDNA-b3556/fastani_result.tsv --threads 1
[2023-03-19 04:11:51,111] [INFO] Task succeeded: fastANI
[2023-03-19 04:11:51,111] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 04:11:51,111] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 04:11:51,111] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 04:11:51,111] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 04:11:51,112] [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
--------------------------------------------------------------------------------
[2023-03-19 04:11:51,175] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3556/tc_result.tsv
[2023-03-19 04:11:51,175] [INFO] ===== Taxonomy check completed =====
[2023-03-19 04:11:51,175] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 04:11:51,175] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/checkm_data
[2023-03-19 04:11:51,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 04:11:51,203] [INFO] Task started: CheckM
[2023-03-19 04:11:51,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3556/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3556/checkm_input OceanDNA-b3556/checkm_result
[2023-03-19 04:12:56,778] [INFO] Task succeeded: CheckM
[2023-03-19 04:12:56,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 3.12%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-19 04:12:56,782] [INFO] ===== Completeness check finished =====
[2023-03-19 04:12:56,782] [INFO] ===== Start GTDB Search =====
[2023-03-19 04:12:56,782] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3556/markers.fasta)
[2023-03-19 04:12:56,782] [INFO] Task started: Blastn
[2023-03-19 04:12:56,782] [INFO] Running command: blastn -query OceanDNA-b3556/markers.fasta -db /var/lib/cwl/stgc0729aa9-2bdb-48b9-ac9a-4d2fa043a180/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3556/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 04:12:57,483] [INFO] Task succeeded: Blastn
[2023-03-19 04:12:57,484] [INFO] Selected 24 target genomes.
[2023-03-19 04:12:57,484] [INFO] Target genome list was writen to OceanDNA-b3556/target_genomes_gtdb.txt
[2023-03-19 04:12:57,826] [INFO] Task started: fastANI
[2023-03-19 04:12:57,826] [INFO] Running command: fastANI --query /var/lib/cwl/stga0b679ea-9fc3-4dec-b444-546fd9574bbd/OceanDNA-b3556.fa --refList OceanDNA-b3556/target_genomes_gtdb.txt --output OceanDNA-b3556/fastani_result_gtdb.tsv --threads 1
[2023-03-19 04:13:10,304] [INFO] Task succeeded: fastANI
[2023-03-19 04:13:10,309] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 04:13:10,309] [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_014860625.1	s__QYOJ01 sp014860625	79.0279	452	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__QYOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783905.1	s__QYOJ01 sp016783905	78.6955	395	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__QYOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016783865.1	s__LJUQ01 sp016783865	77.9812	55	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__SM23-62;g__LJUQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280875.1	s__QYOJ01 sp007280875	77.0711	221	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__QYOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016926765.1	s__QYOJ01 sp016926765	76.8933	172	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__QYOJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903959905.1	s__CAIVAT01 sp903959905	75.95	59	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.98	99.96	0.97	0.97	6	-
GCA_903828645.1	s__CAIVAT01 sp903828645	75.6706	54	1110	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__FEN-979;g__CAIVAT01	95.0	99.44	99.32	0.88	0.87	3	-
--------------------------------------------------------------------------------
[2023-03-19 04:13:10,310] [INFO] GTDB search result was written to OceanDNA-b3556/result_gtdb.tsv
[2023-03-19 04:13:10,310] [INFO] ===== GTDB Search completed =====
[2023-03-19 04:13:10,310] [INFO] DFAST_QC result json was written to OceanDNA-b3556/dqc_result.json
[2023-03-19 04:13:10,311] [INFO] DFAST_QC completed!
[2023-03-19 04:13:10,311] [INFO] Total running time: 0h2m3s