[2023-03-15 22:15:27,733] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:15:27,734] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:15:27,734] [INFO] DQC Reference Directory: /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference
[2023-03-15 22:15:29,360] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:15:29,361] [INFO] Task started: Prodigal
[2023-03-15 22:15:29,361] [INFO] Running command: cat /var/lib/cwl/stg347c28c0-150c-42bb-a401-57bd0d4b6d19/OceanDNA-b28072.fa | prodigal -d OceanDNA-b28072/cds.fna -a OceanDNA-b28072/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:15:47,229] [INFO] Task succeeded: Prodigal
[2023-03-15 22:15:47,230] [INFO] Task started: HMMsearch
[2023-03-15 22:15:47,230] [INFO] Running command: hmmsearch --tblout OceanDNA-b28072/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/reference_markers.hmm OceanDNA-b28072/protein.faa > /dev/null
[2023-03-15 22:15:47,420] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:15:47,420] [INFO] Found 6/6 markers.
[2023-03-15 22:15:47,455] [INFO] Query marker FASTA was written to OceanDNA-b28072/markers.fasta
[2023-03-15 22:15:47,456] [INFO] Task started: Blastn
[2023-03-15 22:15:47,456] [INFO] Running command: blastn -query OceanDNA-b28072/markers.fasta -db /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/reference_markers.fasta -out OceanDNA-b28072/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:15:48,077] [INFO] Task succeeded: Blastn
[2023-03-15 22:15:48,082] [INFO] Selected 26 target genomes.
[2023-03-15 22:15:48,082] [INFO] Target genome list was writen to OceanDNA-b28072/target_genomes.txt
[2023-03-15 22:15:48,096] [INFO] Task started: fastANI
[2023-03-15 22:15:48,096] [INFO] Running command: fastANI --query /var/lib/cwl/stg347c28c0-150c-42bb-a401-57bd0d4b6d19/OceanDNA-b28072.fa --refList OceanDNA-b28072/target_genomes.txt --output OceanDNA-b28072/fastani_result.tsv --threads 1
[2023-03-15 22:16:04,118] [INFO] Task succeeded: fastANI
[2023-03-15 22:16:04,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:16:04,118] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:16:04,130] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:16:04,131] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:16:04,131] [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
Ascidiaceihabitans donghaensis	strain=CECT 8599	GCA_900302465.1	1510460	1510460	type	True	77.4393	210	924	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	77.0399	151	924	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.9695	151	924	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	76.8159	142	924	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	76.7679	109	924	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	76.7608	128	924	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.6116	137	924	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	76.603	120	924	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	76.5973	114	924	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	76.5859	136	924	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	76.5623	105	924	95	below_threshold
Cognatishimia activa	strain=CECT 5113	GCA_001458335.1	1715691	1715691	type	True	76.5464	110	924	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	76.4812	67	924	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	76.3875	69	924	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	76.3533	137	924	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	76.3506	135	924	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	76.2273	77	924	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	76.0099	78	924	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	75.9142	96	924	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	75.8247	71	924	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	75.6788	56	924	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:16:04,132] [INFO] DFAST Taxonomy check result was written to OceanDNA-b28072/tc_result.tsv
[2023-03-15 22:16:04,136] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:16:04,136] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:16:04,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/checkm_data
[2023-03-15 22:16:04,137] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:16:04,142] [INFO] Task started: CheckM
[2023-03-15 22:16:04,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b28072/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b28072/checkm_input OceanDNA-b28072/checkm_result
[2023-03-15 22:16:50,761] [INFO] Task succeeded: CheckM
[2023-03-15 22:16:50,761] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:16:50,789] [INFO] ===== Completeness check finished =====
[2023-03-15 22:16:50,789] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:16:50,789] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b28072/markers.fasta)
[2023-03-15 22:16:50,790] [INFO] Task started: Blastn
[2023-03-15 22:16:50,790] [INFO] Running command: blastn -query OceanDNA-b28072/markers.fasta -db /var/lib/cwl/stgd751826f-6d8b-485b-b1fc-7ed09c69c3ba/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b28072/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:16:51,829] [INFO] Task succeeded: Blastn
[2023-03-15 22:16:51,834] [INFO] Selected 14 target genomes.
[2023-03-15 22:16:51,834] [INFO] Target genome list was writen to OceanDNA-b28072/target_genomes_gtdb.txt
[2023-03-15 22:16:51,928] [INFO] Task started: fastANI
[2023-03-15 22:16:51,928] [INFO] Running command: fastANI --query /var/lib/cwl/stg347c28c0-150c-42bb-a401-57bd0d4b6d19/OceanDNA-b28072.fa --refList OceanDNA-b28072/target_genomes_gtdb.txt --output OceanDNA-b28072/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:17:02,039] [INFO] Task succeeded: fastANI
[2023-03-15 22:17:02,047] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:17:02,048] [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_002478745.1	s__Ascidiaceihabitans sp002478745	99.2566	754	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.75	99.75	0.89	0.89	2	conclusive
GCA_018647275.1	s__Ascidiaceihabitans sp018647275	93.5198	391	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182105.1	s__Ascidiaceihabitans sp905182105	89.54	704	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182355.1	s__Ascidiaceihabitans sp905182355	79.1874	384	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900302465.1	s__Ascidiaceihabitans donghaensis	77.4524	209	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139555.1	s__Sulfitobacter sp013139555	77.0135	118	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.9695	151	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_900313015.1	s__OMPR01 sp900313015	76.9107	93	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__OMPR01	95.0	97.69	97.65	0.92	0.91	5	-
GCF_013282155.1	s__Sulfitobacter sp013282155	76.7805	150	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCF_900116285.1	s__Sulfitobacter marinus	76.7608	128	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.6014	135	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	76.4902	132	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	76.3506	135	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCA_000472185.1	s__HIMB11 sp000472185	76.2179	66	924	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HIMB11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:17:02,049] [INFO] GTDB search result was written to OceanDNA-b28072/result_gtdb.tsv
[2023-03-15 22:17:02,052] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:17:02,057] [INFO] DFAST_QC result json was written to OceanDNA-b28072/dqc_result.json
[2023-03-15 22:17:02,057] [INFO] DFAST_QC completed!
[2023-03-15 22:17:02,057] [INFO] Total running time: 0h1m34s