[2023-03-18 06:37:01,798] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,798] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference
[2023-03-18 06:37:03,368] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:03,369] [INFO] Task started: Prodigal
[2023-03-18 06:37:03,369] [INFO] Running command: cat /var/lib/cwl/stg5aa29aa9-a4eb-43b6-8610-92186b2d3eb0/OceanDNA-b24357.fa | prodigal -d OceanDNA-b24357/cds.fna -a OceanDNA-b24357/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:08,309] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:08,309] [INFO] Task started: HMMsearch
[2023-03-18 06:37:08,309] [INFO] Running command: hmmsearch --tblout OceanDNA-b24357/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/reference_markers.hmm OceanDNA-b24357/protein.faa > /dev/null
[2023-03-18 06:37:08,458] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:08,458] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5aa29aa9-a4eb-43b6-8610-92186b2d3eb0/OceanDNA-b24357.fa]
[2023-03-18 06:37:08,467] [INFO] Query marker FASTA was written to OceanDNA-b24357/markers.fasta
[2023-03-18 06:37:08,467] [INFO] Task started: Blastn
[2023-03-18 06:37:08,467] [INFO] Running command: blastn -query OceanDNA-b24357/markers.fasta -db /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/reference_markers.fasta -out OceanDNA-b24357/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:08,975] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:08,976] [INFO] Selected 16 target genomes.
[2023-03-18 06:37:08,976] [INFO] Target genome list was writen to OceanDNA-b24357/target_genomes.txt
[2023-03-18 06:37:08,984] [INFO] Task started: fastANI
[2023-03-18 06:37:08,984] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa29aa9-a4eb-43b6-8610-92186b2d3eb0/OceanDNA-b24357.fa --refList OceanDNA-b24357/target_genomes.txt --output OceanDNA-b24357/fastani_result.tsv --threads 1
[2023-03-18 06:37:15,704] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:15,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:15,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:15,705] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:15,705] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:15,705] [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 06:37:15,705] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24357/tc_result.tsv
[2023-03-18 06:37:15,706] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:15,706] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:15,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/checkm_data
[2023-03-18 06:37:15,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:15,710] [INFO] Task started: CheckM
[2023-03-18 06:37:15,711] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24357/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24357/checkm_input OceanDNA-b24357/checkm_result
[2023-03-18 06:37:34,119] [INFO] Task succeeded: CheckM
[2023-03-18 06:37:34,120] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.98%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 06:37:34,121] [INFO] ===== Completeness check finished =====
[2023-03-18 06:37:34,121] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:37:34,122] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24357/markers.fasta)
[2023-03-18 06:37:34,123] [INFO] Task started: Blastn
[2023-03-18 06:37:34,123] [INFO] Running command: blastn -query OceanDNA-b24357/markers.fasta -db /var/lib/cwl/stg9014c37f-ae79-4fd0-9c83-c23fc33bb21d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24357/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:34,869] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:34,870] [INFO] Selected 20 target genomes.
[2023-03-18 06:37:34,870] [INFO] Target genome list was writen to OceanDNA-b24357/target_genomes_gtdb.txt
[2023-03-18 06:37:34,951] [INFO] Task started: fastANI
[2023-03-18 06:37:34,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg5aa29aa9-a4eb-43b6-8610-92186b2d3eb0/OceanDNA-b24357.fa --refList OceanDNA-b24357/target_genomes_gtdb.txt --output OceanDNA-b24357/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:37:38,833] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:38,840] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 06:37:38,841] [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_902577425.1	s__MarineAlpha5-Bin3 sp902577425	77.3667	81	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__MarineAlpha5-Bin3	95.0	95.54	95.54	0.86	0.86	2	-
GCA_902596065.1	s__MarineAlpha5-Bin3 sp902596065	77.21	60	244	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_002938255.1	s__MarineAlpha5-Bin3 sp002938255	77.0628	55	244	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	-
GCA_902561355.1	s__AG-337-I02 sp902561355	76.7986	59	244	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_902618015.1	s__AG-337-I02 sp902618015	76.6386	57	244	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_002938205.1	s__AG-337-I02 sp002938205	76.6315	69	244	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__GCA-002718135;g__AG-337-I02	95.0	99.93	99.93	0.95	0.95	2	-
GCA_002938195.1	s__MarineAlpha5-Bin7 sp002938195	76.6314	57	244	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_902585605.1	s__AG-337-I02 sp902585605	76.5684	51	244	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_902607435.1	s__CACLJX01 sp902607435	76.3722	53	244	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_902521315.1	s__AG-337-I02 sp902521315	76.2446	58	244	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_902623255.1	s__AG-337-I02 sp902623255	76.0563	54	244	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_902615625.1	s__AG-337-I02 sp902615625	75.9573	50	244	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	-
--------------------------------------------------------------------------------
[2023-03-18 06:37:38,841] [INFO] GTDB search result was written to OceanDNA-b24357/result_gtdb.tsv
[2023-03-18 06:37:38,841] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:37:38,842] [INFO] DFAST_QC result json was written to OceanDNA-b24357/dqc_result.json
[2023-03-18 06:37:38,842] [INFO] DFAST_QC completed!
[2023-03-18 06:37:38,842] [INFO] Total running time: 0h0m37s