[2023-03-14 12:49:51,794] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:49:51,794] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:49:51,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference
[2023-03-14 12:49:53,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:49:53,144] [INFO] Task started: Prodigal
[2023-03-14 12:49:53,145] [INFO] Running command: cat /var/lib/cwl/stgd2ec3f0c-7df2-4938-a537-ddc849afa2c9/OceanDNA-b11237.fa | prodigal -d OceanDNA-b11237/cds.fna -a OceanDNA-b11237/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:50:10,456] [INFO] Task succeeded: Prodigal
[2023-03-14 12:50:10,456] [INFO] Task started: HMMsearch
[2023-03-14 12:50:10,456] [INFO] Running command: hmmsearch --tblout OceanDNA-b11237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/reference_markers.hmm OceanDNA-b11237/protein.faa > /dev/null
[2023-03-14 12:50:10,649] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:50:10,650] [INFO] Found 6/6 markers.
[2023-03-14 12:50:10,664] [INFO] Query marker FASTA was written to OceanDNA-b11237/markers.fasta
[2023-03-14 12:50:10,665] [INFO] Task started: Blastn
[2023-03-14 12:50:10,665] [INFO] Running command: blastn -query OceanDNA-b11237/markers.fasta -db /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/reference_markers.fasta -out OceanDNA-b11237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:50:11,324] [INFO] Task succeeded: Blastn
[2023-03-14 12:50:11,325] [INFO] Selected 26 target genomes.
[2023-03-14 12:50:11,325] [INFO] Target genome list was writen to OceanDNA-b11237/target_genomes.txt
[2023-03-14 12:50:11,339] [INFO] Task started: fastANI
[2023-03-14 12:50:11,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ec3f0c-7df2-4938-a537-ddc849afa2c9/OceanDNA-b11237.fa --refList OceanDNA-b11237/target_genomes.txt --output OceanDNA-b11237/fastani_result.tsv --threads 1
[2023-03-14 12:50:26,527] [INFO] Task succeeded: fastANI
[2023-03-14 12:50:26,527] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:50:26,527] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:50:26,528] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:50:26,528] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:50:26,528] [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
--------------------------------------------------------------------------------
[2023-03-14 12:50:26,528] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11237/tc_result.tsv
[2023-03-14 12:50:26,529] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:50:26,529] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:50:26,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/checkm_data
[2023-03-14 12:50:26,532] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:50:26,536] [INFO] Task started: CheckM
[2023-03-14 12:50:26,536] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11237/checkm_input OceanDNA-b11237/checkm_result
[2023-03-14 12:51:17,556] [INFO] Task succeeded: CheckM
[2023-03-14 12:51:17,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:51:17,559] [INFO] ===== Completeness check finished =====
[2023-03-14 12:51:17,559] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:51:17,559] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11237/markers.fasta)
[2023-03-14 12:51:17,561] [INFO] Task started: Blastn
[2023-03-14 12:51:17,561] [INFO] Running command: blastn -query OceanDNA-b11237/markers.fasta -db /var/lib/cwl/stg5ff71be1-004d-4e04-856f-4bdb1af6235b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:51:18,459] [INFO] Task succeeded: Blastn
[2023-03-14 12:51:18,461] [INFO] Selected 20 target genomes.
[2023-03-14 12:51:18,461] [INFO] Target genome list was writen to OceanDNA-b11237/target_genomes_gtdb.txt
[2023-03-14 12:51:18,482] [INFO] Task started: fastANI
[2023-03-14 12:51:18,482] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2ec3f0c-7df2-4938-a537-ddc849afa2c9/OceanDNA-b11237.fa --refList OceanDNA-b11237/target_genomes_gtdb.txt --output OceanDNA-b11237/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:51:26,713] [INFO] Task succeeded: fastANI
[2023-03-14 12:51:26,720] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:51:26,720] [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_018647605.1	s__UBA8316 sp018647605	78.4864	264	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623955.1	s__UBA8316 sp018623955	78.4313	159	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009936675.1	s__UBA8316 sp009936675	78.3192	228	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.40	99.39	0.87	0.79	3	-
GCA_002364535.1	s__UBA8316 sp002364535	78.2851	289	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.85	99.85	0.95	0.95	2	-
GCA_002390455.1	s__UBA8316 sp002390455	78.1751	255	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	99.09	98.50	0.88	0.83	3	-
GCA_002687665.1	s__UBA8316 sp002687665	77.7751	138	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002336305.1	s__UBA8316 sp002336305	77.4885	169	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619315.1	s__UBA8316 sp902619315	77.4738	146	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711215.1	s__UBA8316 sp002711215	77.2808	170	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	100.00	100.00	0.95	0.95	2	-
GCA_003538555.1	s__UBA8316 sp003538555	76.9537	102	624	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__UBA8316	95.0	98.54	98.54	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-03-14 12:51:26,721] [INFO] GTDB search result was written to OceanDNA-b11237/result_gtdb.tsv
[2023-03-14 12:51:26,721] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:51:26,722] [INFO] DFAST_QC result json was written to OceanDNA-b11237/dqc_result.json
[2023-03-14 12:51:26,722] [INFO] DFAST_QC completed!
[2023-03-14 12:51:26,722] [INFO] Total running time: 0h1m35s