[2023-03-15 15:55:18,001] [INFO] DFAST_QC pipeline started.
[2023-03-15 15:55:18,001] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 15:55:18,001] [INFO] DQC Reference Directory: /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference
[2023-03-15 15:55:19,112] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 15:55:19,113] [INFO] Task started: Prodigal
[2023-03-15 15:55:19,113] [INFO] Running command: cat /var/lib/cwl/stg89c2bd82-abf4-49fb-8319-d0fe596a0571/OceanDNA-b7636.fa | prodigal -d OceanDNA-b7636/cds.fna -a OceanDNA-b7636/protein.faa -g 11 -q > /dev/null
[2023-03-15 15:55:25,737] [INFO] Task succeeded: Prodigal
[2023-03-15 15:55:25,738] [INFO] Task started: HMMsearch
[2023-03-15 15:55:25,738] [INFO] Running command: hmmsearch --tblout OceanDNA-b7636/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/reference_markers.hmm OceanDNA-b7636/protein.faa > /dev/null
[2023-03-15 15:55:25,944] [INFO] Task succeeded: HMMsearch
[2023-03-15 15:55:25,945] [INFO] Found 6/6 markers.
[2023-03-15 15:55:25,956] [INFO] Query marker FASTA was written to OceanDNA-b7636/markers.fasta
[2023-03-15 15:55:25,956] [INFO] Task started: Blastn
[2023-03-15 15:55:25,956] [INFO] Running command: blastn -query OceanDNA-b7636/markers.fasta -db /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/reference_markers.fasta -out OceanDNA-b7636/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:55:26,541] [INFO] Task succeeded: Blastn
[2023-03-15 15:55:26,542] [INFO] Selected 36 target genomes.
[2023-03-15 15:55:26,542] [INFO] Target genome list was writen to OceanDNA-b7636/target_genomes.txt
[2023-03-15 15:55:26,565] [INFO] Task started: fastANI
[2023-03-15 15:55:26,566] [INFO] Running command: fastANI --query /var/lib/cwl/stg89c2bd82-abf4-49fb-8319-d0fe596a0571/OceanDNA-b7636.fa --refList OceanDNA-b7636/target_genomes.txt --output OceanDNA-b7636/fastani_result.tsv --threads 1
[2023-03-15 15:55:45,576] [INFO] Task succeeded: fastANI
[2023-03-15 15:55:45,576] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 15:55:45,577] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 15:55:45,577] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 15:55:45,577] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 15:55:45,577] [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 15:55:45,577] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7636/tc_result.tsv
[2023-03-15 15:55:45,577] [INFO] ===== Taxonomy check completed =====
[2023-03-15 15:55:45,577] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 15:55:45,577] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/checkm_data
[2023-03-15 15:55:45,580] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 15:55:45,583] [INFO] Task started: CheckM
[2023-03-15 15:55:45,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7636/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7636/checkm_input OceanDNA-b7636/checkm_result
[2023-03-15 15:56:08,125] [INFO] Task succeeded: CheckM
[2023-03-15 15:56:08,125] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 67.94%
Contamintation: 0.98%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 15:56:08,127] [INFO] ===== Completeness check finished =====
[2023-03-15 15:56:08,127] [INFO] ===== Start GTDB Search =====
[2023-03-15 15:56:08,127] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7636/markers.fasta)
[2023-03-15 15:56:08,128] [INFO] Task started: Blastn
[2023-03-15 15:56:08,128] [INFO] Running command: blastn -query OceanDNA-b7636/markers.fasta -db /var/lib/cwl/stgf46c5e36-8671-4857-8dac-6d46b9f1110b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7636/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 15:56:09,158] [INFO] Task succeeded: Blastn
[2023-03-15 15:56:09,159] [INFO] Selected 21 target genomes.
[2023-03-15 15:56:09,159] [INFO] Target genome list was writen to OceanDNA-b7636/target_genomes_gtdb.txt
[2023-03-15 15:56:09,201] [INFO] Task started: fastANI
[2023-03-15 15:56:09,201] [INFO] Running command: fastANI --query /var/lib/cwl/stg89c2bd82-abf4-49fb-8319-d0fe596a0571/OceanDNA-b7636.fa --refList OceanDNA-b7636/target_genomes_gtdb.txt --output OceanDNA-b7636/fastani_result_gtdb.tsv --threads 1
[2023-03-15 15:56:16,053] [INFO] Task succeeded: fastANI
[2023-03-15 15:56:16,063] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 15:56:16,063] [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_002702895.1	s__MAG-121220-bin8 sp002702895	77.6853	171	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239275.1	s__MAG-121220-bin8 sp014239275	77.6614	135	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.08	98.67	0.74	0.67	4	-
GCA_003331265.1	s__MAG-121220-bin8 sp003331265	77.4132	122	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.3378	134	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_902559035.1	s__MAG-121220-bin8 sp902559035	77.2309	97	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	-
GCA_905181705.1	s__MAG-121220-bin8 sp905181705	77.2017	124	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181625.1	s__MAG-121220-bin8 sp905181625	77.0956	86	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	77.0617	93	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	76.9451	86	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_902523635.1	s__MAG-121220-bin8 sp902523635	76.762	60	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	76.686	70	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	76.6219	79	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	76.5317	76	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_002705485.1	s__MAG-121220-bin8 sp002705485	76.48	85	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.79	97.60	0.73	0.71	4	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	76.4493	59	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_002084355.1	s__4572-128 sp002084355	74.7176	55	316	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__4572-128;g__4572-128	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 15:56:16,063] [INFO] GTDB search result was written to OceanDNA-b7636/result_gtdb.tsv
[2023-03-15 15:56:16,063] [INFO] ===== GTDB Search completed =====
[2023-03-15 15:56:16,064] [INFO] DFAST_QC result json was written to OceanDNA-b7636/dqc_result.json
[2023-03-15 15:56:16,065] [INFO] DFAST_QC completed!
[2023-03-15 15:56:16,065] [INFO] Total running time: 0h0m58s