[2023-03-16 21:45:13,163] [INFO] DFAST_QC pipeline started.
[2023-03-16 21:45:13,163] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 21:45:13,164] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference
[2023-03-16 21:45:14,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 21:45:14,283] [INFO] Task started: Prodigal
[2023-03-16 21:45:14,283] [INFO] Running command: cat /var/lib/cwl/stgecf57292-f7e1-48a7-bc0a-a0f949a5cafa/OceanDNA-b35067.fa | prodigal -d OceanDNA-b35067/cds.fna -a OceanDNA-b35067/protein.faa -g 11 -q > /dev/null
[2023-03-16 21:45:35,788] [INFO] Task succeeded: Prodigal
[2023-03-16 21:45:35,788] [INFO] Task started: HMMsearch
[2023-03-16 21:45:35,788] [INFO] Running command: hmmsearch --tblout OceanDNA-b35067/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/reference_markers.hmm OceanDNA-b35067/protein.faa > /dev/null
[2023-03-16 21:45:36,015] [INFO] Task succeeded: HMMsearch
[2023-03-16 21:45:36,016] [INFO] Found 6/6 markers.
[2023-03-16 21:45:36,038] [INFO] Query marker FASTA was written to OceanDNA-b35067/markers.fasta
[2023-03-16 21:45:36,038] [INFO] Task started: Blastn
[2023-03-16 21:45:36,039] [INFO] Running command: blastn -query OceanDNA-b35067/markers.fasta -db /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/reference_markers.fasta -out OceanDNA-b35067/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:45:36,703] [INFO] Task succeeded: Blastn
[2023-03-16 21:45:36,704] [INFO] Selected 29 target genomes.
[2023-03-16 21:45:36,704] [INFO] Target genome list was writen to OceanDNA-b35067/target_genomes.txt
[2023-03-16 21:45:36,719] [INFO] Task started: fastANI
[2023-03-16 21:45:36,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgecf57292-f7e1-48a7-bc0a-a0f949a5cafa/OceanDNA-b35067.fa --refList OceanDNA-b35067/target_genomes.txt --output OceanDNA-b35067/fastani_result.tsv --threads 1
[2023-03-16 21:45:55,716] [INFO] Task succeeded: fastANI
[2023-03-16 21:45:55,716] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 21:45:55,717] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 21:45:55,729] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 21:45:55,729] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 21:45:55,729] [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
Pseudoalteromonas ruthenica	strain=LMG 19699	GCA_008808095.1	151081	151081	type	True	97.3413	1181	1237	95	conclusive
Pseudoalteromonas profundi	strain=CGMCC 1.15394	GCA_014642695.1	1774956	1774956	type	True	77.699	163	1237	95	below_threshold
Pseudoalteromonas amylolytica	strain=JW1	GCA_001854605.1	1859457	1859457	type	True	77.6609	111	1237	95	below_threshold
Pseudoalteromonas gelatinilytica	strain=NH153	GCA_001641615.1	1703256	1703256	type	True	77.6014	170	1237	95	below_threshold
Pseudoalteromonas caenipelagi	strain=JBTF-M23	GCA_013140855.1	2726988	2726988	type	True	77.5216	120	1237	95	below_threshold
Pseudoalteromonas arabiensis	strain=JCM 17292	GCA_001550155.1	874454	874454	type	True	77.4782	147	1237	95	below_threshold
Pseudoalteromonas lipolytica	strain=CGMCC 1.8499	GCA_900116435.1	570156	570156	suspected-type	True	77.3354	162	1237	95	below_threshold
Pseudoalteromonas flavipulchra	strain=LMG 20361	GCA_014596995.1	137779	137779	suspected-type	True	77.2738	137	1237	95	below_threshold
Pseudoalteromonas flavipulchra	strain=NCIMB 2033	GCA_014858715.1	137779	137779	suspected-type	True	77.2709	139	1237	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	77.2544	123	1237	95	below_threshold
Pseudoalteromonas piscicida	strain=JCM 20779	GCA_000238315.4	43662	43662	type	True	77.2536	150	1237	95	below_threshold
Pseudoalteromonas piscicida	strain=ATCC 15057	GCA_000382005.1	43662	43662	type	True	77.2222	148	1237	95	below_threshold
Pseudoalteromonas peptidolytica	strain=DSM 14001	GCA_012641745.1	61150	61150	type	True	77.1997	134	1237	95	below_threshold
Pseudoalteromonas peptidolytica	strain=F12-50-A1	GCA_014858745.1	61150	61150	type	True	77.1958	136	1237	95	below_threshold
Pseudoalteromonas peptidolytica	strain=NBRC 101021	GCA_007989895.1	61150	61150	type	True	77.1938	122	1237	95	below_threshold
Pseudoalteromonas espejiana	strain=NBRC 102222	GCA_007989585.1	28107	28107	type	True	77.1453	126	1237	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_014925335.1	161398	161398	suspected-type	True	77.1437	118	1237	95	below_threshold
Pseudoalteromonas citrea	strain=DSM 8771	GCA_000238375.4	43655	43655	type	True	77.1215	123	1237	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=DSM 6061	GCA_001625655.1	43657	43657	suspected-type	True	77.1152	100	1237	95	below_threshold
Pseudoalteromonas phenolica	strain=KCTC 12086	GCA_001444405.1	161398	161398	suspected-type	True	77.0782	121	1237	95	below_threshold
Pseudoalteromonas espejiana	strain=ATCC 29659	GCA_002221525.1	28107	28107	type	True	77.0699	132	1237	95	below_threshold
Pseudoalteromonas luteoviolacea	strain=CH130	GCA_014925325.1	43657	43657	suspected-type	True	77.0327	104	1237	95	below_threshold
Pseudoalteromonas phenolica	strain=O-BC30	GCA_004103265.1	161398	161398	suspected-type	True	77.0222	115	1237	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 21:45:55,729] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35067/tc_result.tsv
[2023-03-16 21:45:55,729] [INFO] ===== Taxonomy check completed =====
[2023-03-16 21:45:55,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 21:45:55,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/checkm_data
[2023-03-16 21:45:55,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 21:45:55,884] [INFO] Task started: CheckM
[2023-03-16 21:45:55,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35067/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35067/checkm_input OceanDNA-b35067/checkm_result
[2023-03-16 21:46:49,805] [INFO] Task succeeded: CheckM
[2023-03-16 21:46:49,805] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 21:46:49,808] [INFO] ===== Completeness check finished =====
[2023-03-16 21:46:49,808] [INFO] ===== Start GTDB Search =====
[2023-03-16 21:46:49,808] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35067/markers.fasta)
[2023-03-16 21:46:49,808] [INFO] Task started: Blastn
[2023-03-16 21:46:49,808] [INFO] Running command: blastn -query OceanDNA-b35067/markers.fasta -db /var/lib/cwl/stg9b25771f-7d80-4224-8459-5dc5b328bfa7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35067/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 21:46:50,875] [INFO] Task succeeded: Blastn
[2023-03-16 21:46:50,876] [INFO] Selected 17 target genomes.
[2023-03-16 21:46:50,876] [INFO] Target genome list was writen to OceanDNA-b35067/target_genomes_gtdb.txt
[2023-03-16 21:46:50,888] [INFO] Task started: fastANI
[2023-03-16 21:46:50,888] [INFO] Running command: fastANI --query /var/lib/cwl/stgecf57292-f7e1-48a7-bc0a-a0f949a5cafa/OceanDNA-b35067.fa --refList OceanDNA-b35067/target_genomes_gtdb.txt --output OceanDNA-b35067/fastani_result_gtdb.tsv --threads 1
[2023-03-16 21:47:03,549] [INFO] Task succeeded: fastANI
[2023-03-16 21:47:03,559] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 21:47:03,560] [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_008808095.1	s__Pseudoalteromonas ruthenica	97.3456	1180	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.29	0.94	0.91	18	conclusive
GCF_002964765.1	s__Pseudoalteromonas sp002964765	78.9917	372	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	98.12	0.95	0.94	4	-
GCF_002964785.1	s__Pseudoalteromonas sp002964785	78.8943	385	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002964705.1	s__Pseudoalteromonas sp002964705	78.8863	388	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	96.66	96.66	0.91	0.91	2	-
GCF_001641615.1	s__Pseudoalteromonas gelatinilytica	77.6204	169	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.27	97.45	0.92	0.88	6	-
GCF_013140855.1	s__Pseudoalteromonas caenipelagi	77.5216	120	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306915.1	s__Pseudoalteromonas lipolytica_A	77.5059	170	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.22	97.66	0.91	0.90	9	-
GCF_002744175.1	s__Pseudoalteromonas piscicida_B	77.4803	132	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002289345.1	s__Pseudoalteromonas sp002289345	77.4528	134	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.3013	N/A	N/A	N/A	N/A	1	-
GCF_002723455.1	s__Pseudoalteromonas sp002723455	77.4235	138	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.50	98.50	0.93	0.93	2	-
GCF_003590335.1	s__Pseudoalteromonas sp003590335	77.2452	114	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.57	97.56	0.90	0.89	3	-
GCF_005876835.1	s__Pseudoalteromonas phenolica_B	77.224	122	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482385.1	s__Pseudoalteromonas rubra_B	77.121	119	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	95.23	95.23	0.89	0.89	2	-
GCF_001444405.1	s__Pseudoalteromonas phenolica	77.0982	120	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.52	98.61	0.97	0.92	4	-
GCF_002221525.1	s__Pseudoalteromonas espejiana	77.0682	133	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_017638925.1	s__Pseudoalteromonas xiamenensis	76.8525	114	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333235.1	s__Pseudoalteromonas luteoviolacea_D	76.823	105	1237	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 21:47:03,560] [INFO] GTDB search result was written to OceanDNA-b35067/result_gtdb.tsv
[2023-03-16 21:47:03,560] [INFO] ===== GTDB Search completed =====
[2023-03-16 21:47:03,562] [INFO] DFAST_QC result json was written to OceanDNA-b35067/dqc_result.json
[2023-03-16 21:47:03,562] [INFO] DFAST_QC completed!
[2023-03-16 21:47:03,562] [INFO] Total running time: 0h1m50s