[2023-03-16 17:31:39,554] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:31:39,555] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:31:39,555] [INFO] DQC Reference Directory: /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference
[2023-03-16 17:31:42,004] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:31:42,004] [INFO] Task started: Prodigal
[2023-03-16 17:31:42,004] [INFO] Running command: cat /var/lib/cwl/stg8fe4b2e7-fed8-44c0-80f8-b05a2bf9f367/OceanDNA-b9684.fa | prodigal -d OceanDNA-b9684/cds.fna -a OceanDNA-b9684/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:31:59,248] [INFO] Task succeeded: Prodigal
[2023-03-16 17:31:59,248] [INFO] Task started: HMMsearch
[2023-03-16 17:31:59,248] [INFO] Running command: hmmsearch --tblout OceanDNA-b9684/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/reference_markers.hmm OceanDNA-b9684/protein.faa > /dev/null
[2023-03-16 17:31:59,433] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:31:59,434] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8fe4b2e7-fed8-44c0-80f8-b05a2bf9f367/OceanDNA-b9684.fa]
[2023-03-16 17:31:59,459] [INFO] Query marker FASTA was written to OceanDNA-b9684/markers.fasta
[2023-03-16 17:31:59,461] [INFO] Task started: Blastn
[2023-03-16 17:31:59,461] [INFO] Running command: blastn -query OceanDNA-b9684/markers.fasta -db /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/reference_markers.fasta -out OceanDNA-b9684/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:32:00,039] [INFO] Task succeeded: Blastn
[2023-03-16 17:32:00,041] [INFO] Selected 15 target genomes.
[2023-03-16 17:32:00,041] [INFO] Target genome list was writen to OceanDNA-b9684/target_genomes.txt
[2023-03-16 17:32:00,053] [INFO] Task started: fastANI
[2023-03-16 17:32:00,053] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fe4b2e7-fed8-44c0-80f8-b05a2bf9f367/OceanDNA-b9684.fa --refList OceanDNA-b9684/target_genomes.txt --output OceanDNA-b9684/fastani_result.tsv --threads 1
[2023-03-16 17:32:14,230] [INFO] Task succeeded: fastANI
[2023-03-16 17:32:14,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:32:14,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:32:14,239] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 17:32:14,239] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 17:32:14,239] [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
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	98.7618	524	541	95	conclusive
Maribacter arcticus	strain=DSM 23546	GCA_900167935.1	561365	561365	type	True	89.7131	476	541	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	80.2705	346	541	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	80.2464	341	541	95	below_threshold
Maribacter stanieri	strain=DSM 19891	GCA_900112245.1	440514	440514	type	True	80.177	340	541	95	below_threshold
Maribacter aquivivus	strain=DSM 16478	GCA_900142175.1	228958	228958	type	True	80.1758	335	541	95	below_threshold
Maribacter caenipelagi	strain=CECT 8455	GCA_004364175.1	1447781	1447781	type	True	79.9696	328	541	95	below_threshold
Maribacter spongiicola	strain=DSM 25233	GCA_004364165.1	1206753	1206753	type	True	79.7918	338	541	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	79.4223	280	541	95	below_threshold
Maribacter sedimenticola	strain=DSM 19840	GCA_900188415.1	228956	228956	type	True	78.9711	241	541	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:32:14,241] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9684/tc_result.tsv
[2023-03-16 17:32:14,241] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:32:14,241] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:32:14,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/checkm_data
[2023-03-16 17:32:14,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:32:14,247] [INFO] Task started: CheckM
[2023-03-16 17:32:14,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9684/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9684/checkm_input OceanDNA-b9684/checkm_result
[2023-03-16 17:33:02,093] [INFO] Task succeeded: CheckM
[2023-03-16 17:33:02,094] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.22%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 17:33:02,097] [INFO] ===== Completeness check finished =====
[2023-03-16 17:33:02,097] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:33:02,097] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9684/markers.fasta)
[2023-03-16 17:33:02,098] [INFO] Task started: Blastn
[2023-03-16 17:33:02,098] [INFO] Running command: blastn -query OceanDNA-b9684/markers.fasta -db /var/lib/cwl/stg4bd67cef-bffe-4da5-8e29-612364661bb8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9684/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:33:02,985] [INFO] Task succeeded: Blastn
[2023-03-16 17:33:02,986] [INFO] Selected 10 target genomes.
[2023-03-16 17:33:02,986] [INFO] Target genome list was writen to OceanDNA-b9684/target_genomes_gtdb.txt
[2023-03-16 17:33:02,997] [INFO] Task started: fastANI
[2023-03-16 17:33:02,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg8fe4b2e7-fed8-44c0-80f8-b05a2bf9f367/OceanDNA-b9684.fa --refList OceanDNA-b9684/target_genomes_gtdb.txt --output OceanDNA-b9684/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:33:15,430] [INFO] Task succeeded: fastANI
[2023-03-16 17:33:15,436] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 17:33:15,436] [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
GCF_900109345.1	s__Maribacter orientalis	98.7618	524	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900167935.1	s__Maribacter arcticus	89.7131	476	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050675.1	s__Maribacter sp011050675	80.6432	325	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	0.99	0.99	2	-
GCF_005771495.1	s__Maribacter sp005771495	80.5113	345	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001913155.1	s__Maribacter hydrothermalis	80.2464	341	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900112245.1	s__Maribacter stanieri	80.177	340	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_900142175.1	s__Maribacter aquivivus	80.1758	335	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364175.1	s__Maribacter caenipelagi	79.9532	329	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364165.1	s__Maribacter spongiicola	79.7918	338	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188415.1	s__Maribacter sedimenticola	78.9711	241	541	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.95	97.95	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 17:33:15,436] [INFO] GTDB search result was written to OceanDNA-b9684/result_gtdb.tsv
[2023-03-16 17:33:15,437] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:33:15,438] [INFO] DFAST_QC result json was written to OceanDNA-b9684/dqc_result.json
[2023-03-16 17:33:15,438] [INFO] DFAST_QC completed!
[2023-03-16 17:33:15,438] [INFO] Total running time: 0h1m36s