[2024-01-24 13:40:46,146] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:46,149] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:46,149] [INFO] DQC Reference Directory: /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference
[2024-01-24 13:40:47,430] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,431] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,431] [INFO] Running command: gunzip -c /var/lib/cwl/stga55001de-6123-4c01-b6f1-2002ac1dda57/GCF_030159975.1_ASM3015997v1_genomic.fna.gz | prodigal -d GCF_030159975.1_ASM3015997v1_genomic.fna/cds.fna -a GCF_030159975.1_ASM3015997v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:01,836] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:01,836] [INFO] Task started: HMMsearch
[2024-01-24 13:41:01,837] [INFO] Running command: hmmsearch --tblout GCF_030159975.1_ASM3015997v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/reference_markers.hmm GCF_030159975.1_ASM3015997v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,122] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,124] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,170] [INFO] Query marker FASTA was written to GCF_030159975.1_ASM3015997v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,170] [INFO] Task started: Blastn
[2024-01-24 13:41:02,170] [INFO] Running command: blastn -query GCF_030159975.1_ASM3015997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/reference_markers.fasta -out GCF_030159975.1_ASM3015997v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:02,971] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:02,975] [INFO] Selected 19 target genomes.
[2024-01-24 13:41:02,976] [INFO] Target genome list was writen to GCF_030159975.1_ASM3015997v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,012] [INFO] Task started: fastANI
[2024-01-24 13:41:03,013] [INFO] Running command: fastANI --query /var/lib/cwl/stga55001de-6123-4c01-b6f1-2002ac1dda57/GCF_030159975.1_ASM3015997v1_genomic.fna.gz --refList GCF_030159975.1_ASM3015997v1_genomic.fna/target_genomes.txt --output GCF_030159975.1_ASM3015997v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:17,362] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:17,362] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:17,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:17,378] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:17,378] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:17,378] [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 geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	83.5452	989	1452	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	83.5416	1003	1452	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	79.2765	571	1452	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	79.252	573	1452	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	79.002	616	1452	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.825	472	1452	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.8205	465	1452	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	78.4931	457	1452	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	78.3929	562	1452	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	78.3475	382	1452	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	77.8552	438	1452	95	below_threshold
Donghicola tyrosinivorans	strain=DSM 100212	GCA_003003355.1	1652492	1652492	type	True	77.2786	195	1452	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	77.0871	334	1452	95	below_threshold
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	77.0612	266	1452	95	below_threshold
Zongyanglinia marina	strain=DSW4-44	GCA_005771405.1	2578117	2578117	type	True	77.0103	170	1452	95	below_threshold
Zongyanglinia huanghaiensis	strain=CY05	GCA_009753675.1	2682100	2682100	type	True	76.7888	195	1452	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.6777	169	1452	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.2068	168	1452	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.2068	168	1452	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:17,380] [INFO] DFAST Taxonomy check result was written to GCF_030159975.1_ASM3015997v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:17,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:17,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:17,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/checkm_data
[2024-01-24 13:41:17,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:17,430] [INFO] Task started: CheckM
[2024-01-24 13:41:17,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030159975.1_ASM3015997v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030159975.1_ASM3015997v1_genomic.fna/checkm_input GCF_030159975.1_ASM3015997v1_genomic.fna/checkm_result
[2024-01-24 13:42:02,911] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:02,913] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:02,935] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:02,935] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:02,935] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030159975.1_ASM3015997v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:02,936] [INFO] Task started: Blastn
[2024-01-24 13:42:02,936] [INFO] Running command: blastn -query GCF_030159975.1_ASM3015997v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6517e66d-2b92-4dc5-8eac-e9dea1838857/dqc_reference/reference_markers_gtdb.fasta -out GCF_030159975.1_ASM3015997v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:04,344] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:04,352] [INFO] Selected 16 target genomes.
[2024-01-24 13:42:04,352] [INFO] Target genome list was writen to GCF_030159975.1_ASM3015997v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:04,393] [INFO] Task started: fastANI
[2024-01-24 13:42:04,394] [INFO] Running command: fastANI --query /var/lib/cwl/stga55001de-6123-4c01-b6f1-2002ac1dda57/GCF_030159975.1_ASM3015997v1_genomic.fna.gz --refList GCF_030159975.1_ASM3015997v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030159975.1_ASM3015997v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:17,403] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:17,423] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:17,423] [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_000622325.1	s__Sulfitobacter geojensis	83.5452	1002	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	79.6385	444	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_001650875.1	s__Sulfitobacter sp001650875	79.4749	610	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622385.1	s__Sulfitobacter noctilucicola	79.2847	570	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017854855.1	s__Sulfitobacter sp017854855	79.2194	632	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003335585.1	s__Sulfitobacter sp003335585	79.1733	662	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003611275.1	s__Sulfitobacter sp001634775	79.1584	490	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.83	96.27	0.81	0.78	5	-
GCF_016801775.1	s__Sulfitobacter mediterraneus_A	79.152	608	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	100.00	99.99	1.00	1.00	16	-
GCF_000622365.1	s__Sulfitobacter noctilucae	78.9984	617	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363555.1	s__Sulfitobacter sp009363555	78.851	518	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	78.1753	441	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	78.1688	486	1452	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	78.1646	455	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113435.1	s__Sulfitobacter dubius	78.0655	400	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.36	97.36	0.82	0.82	2	-
GCF_000622405.1	s__Sulfitobacter donghicola	77.7822	339	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004342065.1	s__Primorskyibacter sedentarius	77.0517	267	1452	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:17,425] [INFO] GTDB search result was written to GCF_030159975.1_ASM3015997v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:17,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:17,430] [INFO] DFAST_QC result json was written to GCF_030159975.1_ASM3015997v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:17,430] [INFO] DFAST_QC completed!
[2024-01-24 13:42:17,430] [INFO] Total running time: 0h1m31s