[2023-03-19 03:10:00,786] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:10:00,787] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:10:00,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference
[2023-03-19 03:10:01,883] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:10:01,883] [INFO] Task started: Prodigal
[2023-03-19 03:10:01,883] [INFO] Running command: cat /var/lib/cwl/stg41f831bb-3fc7-4d77-b93c-acf2855cdc61/OceanDNA-b25281.fa | prodigal -d OceanDNA-b25281/cds.fna -a OceanDNA-b25281/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:10:05,820] [INFO] Task succeeded: Prodigal
[2023-03-19 03:10:05,821] [INFO] Task started: HMMsearch
[2023-03-19 03:10:05,821] [INFO] Running command: hmmsearch --tblout OceanDNA-b25281/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/reference_markers.hmm OceanDNA-b25281/protein.faa > /dev/null
[2023-03-19 03:10:05,954] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:10:05,955] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg41f831bb-3fc7-4d77-b93c-acf2855cdc61/OceanDNA-b25281.fa]
[2023-03-19 03:10:05,963] [INFO] Query marker FASTA was written to OceanDNA-b25281/markers.fasta
[2023-03-19 03:10:05,963] [INFO] Task started: Blastn
[2023-03-19 03:10:05,963] [INFO] Running command: blastn -query OceanDNA-b25281/markers.fasta -db /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/reference_markers.fasta -out OceanDNA-b25281/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:06,456] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:06,457] [INFO] Selected 12 target genomes.
[2023-03-19 03:10:06,457] [INFO] Target genome list was writen to OceanDNA-b25281/target_genomes.txt
[2023-03-19 03:10:06,463] [INFO] Task started: fastANI
[2023-03-19 03:10:06,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f831bb-3fc7-4d77-b93c-acf2855cdc61/OceanDNA-b25281.fa --refList OceanDNA-b25281/target_genomes.txt --output OceanDNA-b25281/fastani_result.tsv --threads 1
[2023-03-19 03:10:11,170] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:11,170] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:10:11,170] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:10:11,171] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:10:11,171] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 03:10:11,171] [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 03:10:11,171] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25281/tc_result.tsv
[2023-03-19 03:10:11,171] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:10:11,171] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:10:11,171] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/checkm_data
[2023-03-19 03:10:11,174] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:10:11,272] [INFO] Task started: CheckM
[2023-03-19 03:10:11,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25281/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25281/checkm_input OceanDNA-b25281/checkm_result
[2023-03-19 03:10:27,769] [INFO] Task succeeded: CheckM
[2023-03-19 03:10:27,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.61%
Contamintation: 7.53%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-19 03:10:27,771] [INFO] ===== Completeness check finished =====
[2023-03-19 03:10:27,771] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:10:27,771] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25281/markers.fasta)
[2023-03-19 03:10:27,772] [INFO] Task started: Blastn
[2023-03-19 03:10:27,772] [INFO] Running command: blastn -query OceanDNA-b25281/markers.fasta -db /var/lib/cwl/stg1bc214ec-d18b-4afc-86fc-9a6bac293ac4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25281/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:10:28,451] [INFO] Task succeeded: Blastn
[2023-03-19 03:10:28,452] [INFO] Selected 22 target genomes.
[2023-03-19 03:10:28,452] [INFO] Target genome list was writen to OceanDNA-b25281/target_genomes_gtdb.txt
[2023-03-19 03:10:28,474] [INFO] Task started: fastANI
[2023-03-19 03:10:28,474] [INFO] Running command: fastANI --query /var/lib/cwl/stg41f831bb-3fc7-4d77-b93c-acf2855cdc61/OceanDNA-b25281.fa --refList OceanDNA-b25281/target_genomes_gtdb.txt --output OceanDNA-b25281/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:10:32,206] [INFO] Task succeeded: fastANI
[2023-03-19 03:10:32,213] [INFO] Found 10 fastANI hits (2 hits with ANI > circumscription radius)
[2023-03-19 03:10:32,213] [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_902570675.1	s__AG-422-B15 sp902570675	97.4226	117	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	98.46	98.46	0.72	0.72	2	inconclusive
GCA_902525595.1	s__AG-422-B15 sp902525595	95.1629	118	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_902547315.1	s__AG-422-B15 sp902547315	78.6468	67	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.94	99.94	0.82	0.82	2	-
GCA_003213515.1	s__AG-422-B15 sp003213515	78.4413	69	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902614655.1	s__AG-422-B15 sp902614655	78.335	60	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.58	99.58	0.73	0.73	2	-
GCA_902589175.1	s__AG-422-B15 sp902589175	78.2366	69	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	99.52	99.44	0.78	0.76	3	-
GCA_902577765.1	s__AG-422-B15 sp902577765	78.2246	80	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902598405.1	s__AG-422-B15 sp902598405	77.9853	57	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902613805.1	s__AG-422-B15 sp902613805	77.9184	77	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564295.1	s__AG-422-B15 sp902564295	77.7148	59	158	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Pelagibacterales;f__AG-422-B15;g__AG-422-B15	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:10:32,213] [INFO] GTDB search result was written to OceanDNA-b25281/result_gtdb.tsv
[2023-03-19 03:10:32,213] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:10:32,214] [INFO] DFAST_QC result json was written to OceanDNA-b25281/dqc_result.json
[2023-03-19 03:10:32,214] [INFO] DFAST_QC completed!
[2023-03-19 03:10:32,214] [INFO] Total running time: 0h0m31s