[2023-03-18 22:44:57,809] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,809] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,809] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference
[2023-03-18 22:44:58,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:58,938] [INFO] Task started: Prodigal
[2023-03-18 22:44:58,938] [INFO] Running command: cat /var/lib/cwl/stgefa18cfd-e313-432f-b025-d59f53c13074/OceanDNA-b29080.fa | prodigal -d OceanDNA-b29080/cds.fna -a OceanDNA-b29080/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:19,011] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:19,012] [INFO] Task started: HMMsearch
[2023-03-18 22:45:19,012] [INFO] Running command: hmmsearch --tblout OceanDNA-b29080/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/reference_markers.hmm OceanDNA-b29080/protein.faa > /dev/null
[2023-03-18 22:45:19,198] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:19,199] [INFO] Found 6/6 markers.
[2023-03-18 22:45:19,221] [INFO] Query marker FASTA was written to OceanDNA-b29080/markers.fasta
[2023-03-18 22:45:19,222] [INFO] Task started: Blastn
[2023-03-18 22:45:19,222] [INFO] Running command: blastn -query OceanDNA-b29080/markers.fasta -db /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/reference_markers.fasta -out OceanDNA-b29080/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:19,850] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:19,851] [INFO] Selected 34 target genomes.
[2023-03-18 22:45:19,851] [INFO] Target genome list was writen to OceanDNA-b29080/target_genomes.txt
[2023-03-18 22:45:19,870] [INFO] Task started: fastANI
[2023-03-18 22:45:19,870] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa18cfd-e313-432f-b025-d59f53c13074/OceanDNA-b29080.fa --refList OceanDNA-b29080/target_genomes.txt --output OceanDNA-b29080/fastani_result.tsv --threads 1
[2023-03-18 22:45:39,736] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:39,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:39,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:39,752] [INFO] Found 29 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:39,752] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 22:45:39,752] [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
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	76.5063	64	1069	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.3254	57	1069	95	below_threshold
Roseovarius lutimaris	strain=DSM 28463	GCA_900115165.1	1005928	1005928	type	True	76.2211	100	1069	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	76.1874	57	1069	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000819625.1	60890	60890	type	True	76.168	72	1069	95	below_threshold
Phaeobacter gallaeciensis	strain=DSM 26640	GCA_000511385.1	60890	60890	type	True	76.168	72	1069	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	75.9898	83	1069	95	below_threshold
Pseudodonghicola xiamenensis	strain=DSM 18339	GCA_000429365.1	337702	337702	type	True	75.973	67	1069	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.9662	64	1069	95	below_threshold
Tritonibacter multivorans	strain=DSM 26470	GCA_900112515.1	928856	928856	type	True	75.9662	64	1069	95	below_threshold
Roseovarius litoreus	strain=DSM 28249	GCA_900142765.1	1155722	1155722	type	True	75.9638	72	1069	95	below_threshold
Aliiroseovarius sediminilitoris	strain=DSM 29439	GCA_900109955.1	1173584	1173584	type	True	75.9585	51	1069	95	below_threshold
Pacificitalea manganoxidans	strain=DY25	GCA_002504165.1	1411902	1411902	type	True	75.9487	57	1069	95	below_threshold
Roseovarius litorisediminis	strain=CECT 8287	GCA_900172295.1	1312363	1312363	type	True	75.948	77	1069	95	below_threshold
Litorivita pollutaquae	strain=FSX-11	GCA_003205515.1	2200892	2200892	type	True	75.9478	71	1069	95	below_threshold
Pseudophaeobacter arcticus	strain=DSM 23566	GCA_000473205.1	385492	385492	type	True	75.9436	79	1069	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	75.9345	82	1069	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	75.9197	71	1069	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	75.8712	72	1069	95	below_threshold
Pseudopuniceibacterium antarcticum	strain=HQ09	GCA_014899185.1	2613965	2613965	type	True	75.8273	59	1069	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	75.7856	59	1069	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	75.7685	77	1069	95	below_threshold
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	75.7502	80	1069	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	75.7493	56	1069	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	75.6732	66	1069	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	75.6249	63	1069	95	below_threshold
Sulfitobacter maritimus	strain=S0837	GCA_013346665.1	2741719	2741719	type	True	75.5781	71	1069	95	below_threshold
Sulfitobacter undariae	strain=DSM 102234	GCA_014196805.1	1563671	1563671	type	True	75.45	56	1069	95	below_threshold
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	75.3603	67	1069	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 22:45:39,752] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29080/tc_result.tsv
[2023-03-18 22:45:39,752] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:39,752] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:39,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/checkm_data
[2023-03-18 22:45:39,753] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:39,758] [INFO] Task started: CheckM
[2023-03-18 22:45:39,758] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29080/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29080/checkm_input OceanDNA-b29080/checkm_result
[2023-03-18 22:46:31,344] [INFO] Task succeeded: CheckM
[2023-03-18 22:46:31,344] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 22:46:31,347] [INFO] ===== Completeness check finished =====
[2023-03-18 22:46:31,347] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:46:31,347] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29080/markers.fasta)
[2023-03-18 22:46:31,348] [INFO] Task started: Blastn
[2023-03-18 22:46:31,348] [INFO] Running command: blastn -query OceanDNA-b29080/markers.fasta -db /var/lib/cwl/stgd3f4b565-e070-47e0-8e4d-1cd9bfc83f65/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29080/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:46:32,405] [INFO] Task succeeded: Blastn
[2023-03-18 22:46:32,406] [INFO] Selected 24 target genomes.
[2023-03-18 22:46:32,406] [INFO] Target genome list was writen to OceanDNA-b29080/target_genomes_gtdb.txt
[2023-03-18 22:46:32,467] [INFO] Task started: fastANI
[2023-03-18 22:46:32,468] [INFO] Running command: fastANI --query /var/lib/cwl/stgefa18cfd-e313-432f-b025-d59f53c13074/OceanDNA-b29080.fa --refList OceanDNA-b29080/target_genomes_gtdb.txt --output OceanDNA-b29080/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:46:48,375] [INFO] Task succeeded: fastANI
[2023-03-18 22:46:48,387] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 22:46:48,387] [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_002336405.1	s__CPC320 sp002336405	99.4559	801	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.74	97.78	0.79	0.51	9	conclusive
GCA_002684375.1	s__CPC320 sp002684375	86.6378	800	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CPC320	95.0	98.52	98.26	0.79	0.72	8	-
GCF_900176485.1	s__Primorskyibacter flagellatus_A	76.3733	71	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110775.1	s__Litorimicrobium taeanense	76.3194	100	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Litorimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115165.1	s__Roseovarius lutimaris	76.2211	100	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000152625.1	s__Roseovarius nubinhibens	76.1268	93	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	96.78	96.50	0.89	0.84	4	-
GCF_900109455.1	s__Roseovarius azorensis	76.0445	69	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	76.0004	72	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	75.9898	83	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_001458415.1	s__Epibacterium multivorans	75.9662	64	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Epibacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	75.9641	83	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142765.1	s__Roseovarius litoreus	75.9638	72	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	95.85	95.85	0.86	0.86	2	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	75.954	81	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_900109035.1	s__Cribrihabitans marinus	75.9197	71	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016778765.1	s__LGRT01 sp016778765	75.9136	80	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LGRT01	95.0	98.26	96.00	0.81	0.61	8	-
GCF_018599245.1	s__Aliiroseovarius lamellibrachiae	75.8279	55	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliiroseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004803475.1	s__Aliishimia ponticola	75.7856	59	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	75.7502	80	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006064855.1	s__Sulfitobacter sp006064855	75.6789	63	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	75.6732	66	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182615.1	s__Ruegeria faecimaris	75.5553	65	1069	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:46:48,387] [INFO] GTDB search result was written to OceanDNA-b29080/result_gtdb.tsv
[2023-03-18 22:46:48,388] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:46:48,390] [INFO] DFAST_QC result json was written to OceanDNA-b29080/dqc_result.json
[2023-03-18 22:46:48,390] [INFO] DFAST_QC completed!
[2023-03-18 22:46:48,390] [INFO] Total running time: 0h1m51s