[2023-03-16 08:12:41,242] [INFO] DFAST_QC pipeline started.
[2023-03-16 08:12:41,242] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 08:12:41,242] [INFO] DQC Reference Directory: /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference
[2023-03-16 08:12:42,349] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 08:12:42,349] [INFO] Task started: Prodigal
[2023-03-16 08:12:42,349] [INFO] Running command: cat /var/lib/cwl/stgc5eaa1ed-4c49-43e2-bed7-ad47f6282904/OceanDNA-b36076.fa | prodigal -d OceanDNA-b36076/cds.fna -a OceanDNA-b36076/protein.faa -g 11 -q > /dev/null
[2023-03-16 08:13:08,628] [INFO] Task succeeded: Prodigal
[2023-03-16 08:13:08,628] [INFO] Task started: HMMsearch
[2023-03-16 08:13:08,628] [INFO] Running command: hmmsearch --tblout OceanDNA-b36076/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/reference_markers.hmm OceanDNA-b36076/protein.faa > /dev/null
[2023-03-16 08:13:08,873] [INFO] Task succeeded: HMMsearch
[2023-03-16 08:13:08,874] [INFO] Found 6/6 markers.
[2023-03-16 08:13:08,896] [INFO] Query marker FASTA was written to OceanDNA-b36076/markers.fasta
[2023-03-16 08:13:08,897] [INFO] Task started: Blastn
[2023-03-16 08:13:08,897] [INFO] Running command: blastn -query OceanDNA-b36076/markers.fasta -db /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/reference_markers.fasta -out OceanDNA-b36076/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:13:09,735] [INFO] Task succeeded: Blastn
[2023-03-16 08:13:09,767] [INFO] Selected 27 target genomes.
[2023-03-16 08:13:09,767] [INFO] Target genome list was writen to OceanDNA-b36076/target_genomes.txt
[2023-03-16 08:13:09,884] [INFO] Task started: fastANI
[2023-03-16 08:13:09,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5eaa1ed-4c49-43e2-bed7-ad47f6282904/OceanDNA-b36076.fa --refList OceanDNA-b36076/target_genomes.txt --output OceanDNA-b36076/fastani_result.tsv --threads 1
[2023-03-16 08:13:26,679] [INFO] Task succeeded: fastANI
[2023-03-16 08:13:26,680] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 08:13:26,680] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 08:13:26,694] [INFO] Found 26 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 08:13:26,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 08:13:26,694] [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
Solimonas fluminis	strain=HR-BB	GCA_002930645.1	2086571	2086571	type	True	77.2267	258	1213	95	below_threshold
Solimonas aquatica	strain=DSM 25927	GCA_900111015.1	489703	489703	type	True	77.0893	220	1213	95	below_threshold
Solimonas soli	strain=DSM 21787	GCA_000474945.1	413479	413479	type	True	76.9113	190	1213	95	below_threshold
Algiphilus aromaticivorans	strain=DG1253	GCA_000733765.1	382454	382454	type	True	76.8814	151	1213	95	below_threshold
Solimonas flava	strain=DSM 18980	GCA_000426685.1	415849	415849	type	True	76.8781	216	1213	95	below_threshold
Solimonas marina	strain=C16B3	GCA_012241385.1	2714601	2714601	type	True	76.8572	162	1213	95	below_threshold
Solimonas variicoloris	strain=DSM 15731	GCA_000382285.1	254408	254408	type	True	76.8277	202	1213	95	below_threshold
Flagellatimonas centrodinii	strain=R2A-3	GCA_016918765.2	2806210	2806210	type	True	76.7668	146	1213	95	below_threshold
Polycyclovorans algicola	strain=TG408	GCA_000711245.1	616992	616992	type	True	76.6548	117	1213	95	below_threshold
Hydrocarboniphaga effusa	strain=AP103	GCA_000271305.1	243629	243629	type	True	76.6122	156	1213	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	76.5438	103	1213	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	76.5278	70	1213	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.4964	81	1213	95	below_threshold
Pseudomonas oryzae	strain=KCTC 32247	GCA_900104805.1	1392877	1392877	type	True	76.486	131	1213	95	below_threshold
Thioalkalivibrio thiocyanoxidans	strain=ARh2	GCA_000385215.1	152475	152475	type	True	76.4762	85	1213	95	below_threshold
Thioalkalivibrio halophilus	strain=HL17	GCA_001995255.1	252474	252474	type	True	76.3448	75	1213	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	76.3416	105	1213	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	76.3324	135	1213	95	below_threshold
Xanthomonas melonis	strain=NCPPB 3434	GCA_020783655.1	56456	56456	type	True	76.3182	108	1213	95	below_threshold
Thioalkalivibrio versutus	strain=AL 2	GCA_001999325.1	106634	106634	type	True	76.174	88	1213	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.0717	161	1213	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.9977	153	1213	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	75.9227	115	1213	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	75.9054	96	1213	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	75.9051	119	1213	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	75.1045	55	1213	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 08:13:26,697] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36076/tc_result.tsv
[2023-03-16 08:13:26,697] [INFO] ===== Taxonomy check completed =====
[2023-03-16 08:13:26,697] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 08:13:26,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/checkm_data
[2023-03-16 08:13:26,698] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 08:13:26,705] [INFO] Task started: CheckM
[2023-03-16 08:13:26,705] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36076/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36076/checkm_input OceanDNA-b36076/checkm_result
[2023-03-16 08:14:31,802] [INFO] Task succeeded: CheckM
[2023-03-16 08:14:31,803] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 08:14:31,846] [INFO] ===== Completeness check finished =====
[2023-03-16 08:14:31,846] [INFO] ===== Start GTDB Search =====
[2023-03-16 08:14:31,847] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36076/markers.fasta)
[2023-03-16 08:14:31,849] [INFO] Task started: Blastn
[2023-03-16 08:14:31,849] [INFO] Running command: blastn -query OceanDNA-b36076/markers.fasta -db /var/lib/cwl/stg78af0809-b55d-466b-9e91-0fd4958f0743/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36076/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 08:14:33,584] [INFO] Task succeeded: Blastn
[2023-03-16 08:14:33,590] [INFO] Selected 26 target genomes.
[2023-03-16 08:14:33,590] [INFO] Target genome list was writen to OceanDNA-b36076/target_genomes_gtdb.txt
[2023-03-16 08:14:33,614] [INFO] Task started: fastANI
[2023-03-16 08:14:33,614] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5eaa1ed-4c49-43e2-bed7-ad47f6282904/OceanDNA-b36076.fa --refList OceanDNA-b36076/target_genomes_gtdb.txt --output OceanDNA-b36076/fastani_result_gtdb.tsv --threads 1
[2023-03-16 08:14:49,435] [INFO] Task succeeded: fastANI
[2023-03-16 08:14:49,448] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 08:14:49,449] [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_002930645.1	s__Solimonas_A fluminis	77.2267	258	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008012115.1	s__Stenotrophobium sp008012115	77.1531	226	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stenotrophobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003428335.1	s__Solimonas_A sp003428335	77.1515	259	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016182805.1	s__JACPFV01 sp016182805	77.087	182	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__JACPFV01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111015.1	s__Solimonas aquatica	77.0774	221	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779605.1	s__Nevskia sp016779605	76.9771	196	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201205.1	s__Sinimarinibacterium flocculans	76.9699	223	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Sinimarinibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003730135.1	s__Stagnimonas aquatica	76.889	234	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Stagnimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733765.1	s__Algiphilus aromaticivorans	76.8814	151	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Algiphilaceae;g__Algiphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047655.1	s__CAU-1509 sp005047655	76.8329	157	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__CAU-1509	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382285.1	s__Solimonas variicoloris	76.8275	202	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Solimonas	95.0372	N/A	N/A	N/A	N/A	1	-
GCF_000381945.1	s__Thioalkalivibrio sp000381945	76.6958	78	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903970595.1	s__Nevskia sp903970595	76.6814	176	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706265.1	s__Polycyclovorans sp002706265	76.637	157	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	99.22	98.54	0.87	0.78	3	-
GCF_000711245.1	s__Polycyclovorans algicola	76.636	118	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Polycyclovorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271305.1	s__Hydrocarboniphaga effusa	76.6122	156	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Hydrocarboniphaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000377785.1	s__Thioalkalivibrio sp000377785	76.5665	82	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104805.1	s__Pseudomonas_K oryzae	76.5006	130	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_K	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378305.1	s__Thioalkalivibrio sp000378305	76.4307	82	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	98.92	98.55	0.95	0.94	12	-
GCF_015356855.1	s__Alcanivorax venustensis	76.3594	104	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	76.3456	134	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_001995255.1	s__Thioalkalivibrio halophilus	76.3448	75	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	96.06	95.07	0.84	0.81	11	-
GCF_013620825.1	s__Rhodanobacter sp001899565	76.1806	106	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCA_903970615.1	s__Nevskia sp903970615	76.1796	91	1213	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Nevskiaceae;g__Nevskia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 08:14:49,453] [INFO] GTDB search result was written to OceanDNA-b36076/result_gtdb.tsv
[2023-03-16 08:14:49,455] [INFO] ===== GTDB Search completed =====
[2023-03-16 08:14:49,460] [INFO] DFAST_QC result json was written to OceanDNA-b36076/dqc_result.json
[2023-03-16 08:14:49,460] [INFO] DFAST_QC completed!
[2023-03-16 08:14:49,460] [INFO] Total running time: 0h2m8s