[2023-03-15 23:38:54,870] [INFO] DFAST_QC pipeline started.
[2023-03-15 23:38:54,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 23:38:54,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference
[2023-03-15 23:38:55,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 23:38:55,972] [INFO] Task started: Prodigal
[2023-03-15 23:38:55,972] [INFO] Running command: cat /var/lib/cwl/stga661d63c-e6fb-4ba1-9a18-234e04b0abbc/OceanDNA-b30177.fa | prodigal -d OceanDNA-b30177/cds.fna -a OceanDNA-b30177/protein.faa -g 11 -q > /dev/null
[2023-03-15 23:39:19,263] [INFO] Task succeeded: Prodigal
[2023-03-15 23:39:19,263] [INFO] Task started: HMMsearch
[2023-03-15 23:39:19,264] [INFO] Running command: hmmsearch --tblout OceanDNA-b30177/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/reference_markers.hmm OceanDNA-b30177/protein.faa > /dev/null
[2023-03-15 23:39:19,496] [INFO] Task succeeded: HMMsearch
[2023-03-15 23:39:19,496] [INFO] Found 6/6 markers.
[2023-03-15 23:39:19,613] [INFO] Query marker FASTA was written to OceanDNA-b30177/markers.fasta
[2023-03-15 23:39:19,615] [INFO] Task started: Blastn
[2023-03-15 23:39:19,615] [INFO] Running command: blastn -query OceanDNA-b30177/markers.fasta -db /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/reference_markers.fasta -out OceanDNA-b30177/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:39:20,322] [INFO] Task succeeded: Blastn
[2023-03-15 23:39:20,335] [INFO] Selected 23 target genomes.
[2023-03-15 23:39:20,335] [INFO] Target genome list was writen to OceanDNA-b30177/target_genomes.txt
[2023-03-15 23:39:20,348] [INFO] Task started: fastANI
[2023-03-15 23:39:20,349] [INFO] Running command: fastANI --query /var/lib/cwl/stga661d63c-e6fb-4ba1-9a18-234e04b0abbc/OceanDNA-b30177.fa --refList OceanDNA-b30177/target_genomes.txt --output OceanDNA-b30177/fastani_result.tsv --threads 1
[2023-03-15 23:39:35,237] [INFO] Task succeeded: fastANI
[2023-03-15 23:39:35,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 23:39:35,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 23:39:35,251] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 23:39:35,251] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 23:39:35,251] [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
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	79.351	432	1224	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	79.2993	454	1224	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	78.7024	399	1224	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.6577	239	1224	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.2878	212	1224	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	77.2788	225	1224	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	77.2648	228	1224	95	below_threshold
Sulfitobacter delicatus	strain=DSM 16477	GCA_900102535.1	218672	218672	type	True	77.2389	213	1224	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.1918	223	1224	95	below_threshold
Sulfitobacter dubius	strain=DSM 16472	GCA_900113435.1	218673	218673	type	True	77.1607	214	1224	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.1377	229	1224	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.1204	228	1224	95	below_threshold
Sulfitobacter donghicola	strain=JCM 14565	GCA_000712275.1	421000	421000	type	True	76.9519	169	1224	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	76.9133	207	1224	95	below_threshold
Sulfitobacter donghicola	strain=KCTC 12864	GCA_000622405.1	421000	421000	type	True	76.8985	171	1224	95	below_threshold
Puniceibacterium sediminis	strain=DSM 29052	GCA_900188035.1	1608407	1608407	type	True	76.5687	119	1224	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	76.1044	94	1224	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.0844	79	1224	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	75.9667	118	1224	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	75.9153	74	1224	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	75.8863	113	1224	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	75.8401	83	1224	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 23:39:35,391] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30177/tc_result.tsv
[2023-03-15 23:39:35,404] [INFO] ===== Taxonomy check completed =====
[2023-03-15 23:39:35,405] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 23:39:35,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/checkm_data
[2023-03-15 23:39:35,406] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 23:39:35,429] [INFO] Task started: CheckM
[2023-03-15 23:39:35,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30177/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30177/checkm_input OceanDNA-b30177/checkm_result
[2023-03-15 23:40:33,626] [INFO] Task succeeded: CheckM
[2023-03-15 23:40:33,626] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 23:40:33,668] [INFO] ===== Completeness check finished =====
[2023-03-15 23:40:33,668] [INFO] ===== Start GTDB Search =====
[2023-03-15 23:40:33,668] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30177/markers.fasta)
[2023-03-15 23:40:33,670] [INFO] Task started: Blastn
[2023-03-15 23:40:33,670] [INFO] Running command: blastn -query OceanDNA-b30177/markers.fasta -db /var/lib/cwl/stg2c6a9958-0d02-41ac-9669-42ffd0733f55/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30177/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 23:40:34,852] [INFO] Task succeeded: Blastn
[2023-03-15 23:40:34,866] [INFO] Selected 11 target genomes.
[2023-03-15 23:40:34,866] [INFO] Target genome list was writen to OceanDNA-b30177/target_genomes_gtdb.txt
[2023-03-15 23:40:34,891] [INFO] Task started: fastANI
[2023-03-15 23:40:34,891] [INFO] Running command: fastANI --query /var/lib/cwl/stga661d63c-e6fb-4ba1-9a18-234e04b0abbc/OceanDNA-b30177.fa --refList OceanDNA-b30177/target_genomes_gtdb.txt --output OceanDNA-b30177/fastani_result_gtdb.tsv --threads 1
[2023-03-15 23:40:43,264] [INFO] Task succeeded: fastANI
[2023-03-15 23:40:43,271] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 23:40:43,271] [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_011050655.1	s__Sulfitobacter sp011050655	97.353	984	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002731875.1	s__Sulfitobacter sp002731875	86.3318	1018	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	-
GCF_900103185.1	s__Sulfitobacter litoralis	79.3616	431	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCF_900106935.1	s__Sulfitobacter pontiacus	79.3198	452	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_013282155.1	s__Sulfitobacter sp013282155	79.2395	455	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_013139555.1	s__Sulfitobacter sp013139555	78.9041	368	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000156335.1	s__Sulfitobacter sp000156335	78.8765	449	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	78.7125	398	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	76.9133	207	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188035.1	s__Puniceibacterium sediminis	76.5839	117	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006265095.1	s__Epibacterium sp006265095	76.1425	114	1224	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 23:40:43,288] [INFO] GTDB search result was written to OceanDNA-b30177/result_gtdb.tsv
[2023-03-15 23:40:43,312] [INFO] ===== GTDB Search completed =====
[2023-03-15 23:40:43,330] [INFO] DFAST_QC result json was written to OceanDNA-b30177/dqc_result.json
[2023-03-15 23:40:43,330] [INFO] DFAST_QC completed!
[2023-03-15 23:40:43,330] [INFO] Total running time: 0h1m48s