[2023-03-17 06:30:49,106] [INFO] DFAST_QC pipeline started.
[2023-03-17 06:30:49,106] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 06:30:49,106] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference
[2023-03-17 06:30:50,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 06:30:50,293] [INFO] Task started: Prodigal
[2023-03-17 06:30:50,293] [INFO] Running command: cat /var/lib/cwl/stg49d0674e-bd74-4050-8f4a-fca0ffd1dc49/OceanDNA-b24379.fa | prodigal -d OceanDNA-b24379/cds.fna -a OceanDNA-b24379/protein.faa -g 11 -q > /dev/null
[2023-03-17 06:30:56,528] [INFO] Task succeeded: Prodigal
[2023-03-17 06:30:56,528] [INFO] Task started: HMMsearch
[2023-03-17 06:30:56,529] [INFO] Running command: hmmsearch --tblout OceanDNA-b24379/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/reference_markers.hmm OceanDNA-b24379/protein.faa > /dev/null
[2023-03-17 06:30:56,702] [INFO] Task succeeded: HMMsearch
[2023-03-17 06:30:56,703] [INFO] Found 6/6 markers.
[2023-03-17 06:30:56,713] [INFO] Query marker FASTA was written to OceanDNA-b24379/markers.fasta
[2023-03-17 06:30:56,713] [INFO] Task started: Blastn
[2023-03-17 06:30:56,713] [INFO] Running command: blastn -query OceanDNA-b24379/markers.fasta -db /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/reference_markers.fasta -out OceanDNA-b24379/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:30:57,248] [INFO] Task succeeded: Blastn
[2023-03-17 06:30:57,249] [INFO] Selected 20 target genomes.
[2023-03-17 06:30:57,249] [INFO] Target genome list was writen to OceanDNA-b24379/target_genomes.txt
[2023-03-17 06:30:57,258] [INFO] Task started: fastANI
[2023-03-17 06:30:57,258] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d0674e-bd74-4050-8f4a-fca0ffd1dc49/OceanDNA-b24379.fa --refList OceanDNA-b24379/target_genomes.txt --output OceanDNA-b24379/fastani_result.tsv --threads 1
[2023-03-17 06:31:06,296] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:06,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 06:31:06,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 06:31:06,297] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 06:31:06,297] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 06:31:06,297] [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 06:31:06,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24379/tc_result.tsv
[2023-03-17 06:31:06,297] [INFO] ===== Taxonomy check completed =====
[2023-03-17 06:31:06,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 06:31:06,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/checkm_data
[2023-03-17 06:31:06,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 06:31:06,302] [INFO] Task started: CheckM
[2023-03-17 06:31:06,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24379/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24379/checkm_input OceanDNA-b24379/checkm_result
[2023-03-17 06:31:27,488] [INFO] Task succeeded: CheckM
[2023-03-17 06:31:27,488] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 06:31:27,490] [INFO] ===== Completeness check finished =====
[2023-03-17 06:31:27,490] [INFO] ===== Start GTDB Search =====
[2023-03-17 06:31:27,490] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24379/markers.fasta)
[2023-03-17 06:31:27,490] [INFO] Task started: Blastn
[2023-03-17 06:31:27,490] [INFO] Running command: blastn -query OceanDNA-b24379/markers.fasta -db /var/lib/cwl/stgf5a98ce4-6ae3-43fc-ae7e-ab04c966a84d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24379/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 06:31:28,387] [INFO] Task succeeded: Blastn
[2023-03-17 06:31:28,388] [INFO] Selected 23 target genomes.
[2023-03-17 06:31:28,388] [INFO] Target genome list was writen to OceanDNA-b24379/target_genomes_gtdb.txt
[2023-03-17 06:31:28,767] [INFO] Task started: fastANI
[2023-03-17 06:31:28,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg49d0674e-bd74-4050-8f4a-fca0ffd1dc49/OceanDNA-b24379.fa --refList OceanDNA-b24379/target_genomes_gtdb.txt --output OceanDNA-b24379/fastani_result_gtdb.tsv --threads 1
[2023-03-17 06:31:34,369] [INFO] Task succeeded: fastANI
[2023-03-17 06:31:34,376] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 06:31:34,376] [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_002938255.1	s__MarineAlpha5-Bin3 sp002938255	99.2777	228	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	98.64	97.83	0.78	0.73	3	conclusive
GCA_902607435.1	s__CACLJX01 sp902607435	79.6712	139	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACLJX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	76.5652	70	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin7	95.0	99.81	99.67	0.81	0.76	3	-
GCA_902596065.1	s__MarineAlpha5-Bin3 sp902596065	76.406	78	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902635455.1	s__CACPNW01 sp902635455	76.3223	71	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__CACPNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718135.1	s__AG-337-I02 sp002718135	76.3046	54	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902577905.1	s__AG-337-I02 sp902577905	76.1271	60	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601455.1	s__AG-337-I02 sp902601455	76.0331	72	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902522015.1	s__AG-337-I02 sp902522015	75.8737	52	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902591485.1	s__AG-337-I02 sp902591485	75.7588	73	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	97.00	97.00	0.77	0.77	2	-
GCA_002937855.1	s__MarineAlpha5-Bin12 sp002937855	75.6666	56	403	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin12	95.0	99.77	99.77	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2023-03-17 06:31:34,376] [INFO] GTDB search result was written to OceanDNA-b24379/result_gtdb.tsv
[2023-03-17 06:31:34,376] [INFO] ===== GTDB Search completed =====
[2023-03-17 06:31:34,377] [INFO] DFAST_QC result json was written to OceanDNA-b24379/dqc_result.json
[2023-03-17 06:31:34,377] [INFO] DFAST_QC completed!
[2023-03-17 06:31:34,378] [INFO] Total running time: 0h0m45s