[2023-03-17 23:49:09,969] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:49:09,969] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:49:09,969] [INFO] DQC Reference Directory: /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference
[2023-03-17 23:49:11,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:49:11,100] [INFO] Task started: Prodigal
[2023-03-17 23:49:11,100] [INFO] Running command: cat /var/lib/cwl/stgabb15b97-a449-44fc-845c-4d0eef3132dd/OceanDNA-b11411.fa | prodigal -d OceanDNA-b11411/cds.fna -a OceanDNA-b11411/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:49:32,206] [INFO] Task succeeded: Prodigal
[2023-03-17 23:49:32,207] [INFO] Task started: HMMsearch
[2023-03-17 23:49:32,207] [INFO] Running command: hmmsearch --tblout OceanDNA-b11411/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/reference_markers.hmm OceanDNA-b11411/protein.faa > /dev/null
[2023-03-17 23:49:32,409] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:49:32,409] [INFO] Found 6/6 markers.
[2023-03-17 23:49:32,430] [INFO] Query marker FASTA was written to OceanDNA-b11411/markers.fasta
[2023-03-17 23:49:32,431] [INFO] Task started: Blastn
[2023-03-17 23:49:32,431] [INFO] Running command: blastn -query OceanDNA-b11411/markers.fasta -db /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/reference_markers.fasta -out OceanDNA-b11411/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:33,087] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:33,088] [INFO] Selected 24 target genomes.
[2023-03-17 23:49:33,088] [INFO] Target genome list was writen to OceanDNA-b11411/target_genomes.txt
[2023-03-17 23:49:33,106] [INFO] Task started: fastANI
[2023-03-17 23:49:33,106] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb15b97-a449-44fc-845c-4d0eef3132dd/OceanDNA-b11411.fa --refList OceanDNA-b11411/target_genomes.txt --output OceanDNA-b11411/fastani_result.tsv --threads 1
[2023-03-17 23:49:48,491] [INFO] Task succeeded: fastANI
[2023-03-17 23:49:48,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:49:48,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:49:48,504] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:49:48,504] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:49:48,504] [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
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	78.7422	391	1111	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	78.7318	392	1111	95	below_threshold
Winogradskyella algicola	strain=IMCC33238	GCA_005869935.1	2575815	2575815	type	True	78.6479	425	1111	95	below_threshold
Winogradskyella thalassocola	strain=DSM 15363	GCA_900099995.1	262004	262004	type	True	78.5016	317	1111	95	below_threshold
Winogradskyella flava	strain=KCTC 52348	GCA_014243395.1	1884876	1884876	type	True	78.399	348	1111	95	below_threshold
Winogradskyella litoriviva	strain=KMM6491	GCA_013249065.1	1220182	1220182	type	True	78.3462	355	1111	95	below_threshold
Winogradskyella sediminis	strain=DSM 28134	GCA_003387355.1	1382466	1382466	type	True	78.2198	314	1111	95	below_threshold
Winogradskyella psychrotolerans	strain=RS-3	GCA_000427335.1	1344585	1344585	type	True	78.1886	324	1111	95	below_threshold
Winogradskyella endarachnes	strain=HL2-2	GCA_009741275.1	2681965	2681965	type	True	78.1881	355	1111	95	below_threshold
Winogradskyella tangerina	strain=M1309	GCA_003260205.1	2023240	2023240	type	True	78.0977	321	1111	95	below_threshold
Winogradskyella jejuensis	strain=DSM 25330	GCA_900129745.1	1089305	1089305	type	True	78.061	266	1111	95	below_threshold
Winogradskyella vidalii	strain=HL634	GCA_013403955.1	2615024	2615024	type	True	77.9582	295	1111	95	below_threshold
Winogradskyella costae	strain=Z3138	GCA_013403865.1	2697008	2697008	type	True	77.9252	306	1111	95	below_threshold
Winogradskyella haliclonae	strain=CCM 8681	GCA_014635865.1	2048558	2048558	type	True	77.8227	291	1111	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.747	144	1111	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	77.4781	234	1111	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.3307	197	1111	95	below_threshold
Hyunsoonleella pacifica	strain=SW033	GCA_004310335.1	1080224	1080224	type	True	77.327	178	1111	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.2696	100	1111	95	below_threshold
Tamlana nanhaiensis	strain=FHC16	GCA_000943555.1	1382798	1382798	type	True	77.2579	175	1111	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.1618	158	1111	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.1035	184	1111	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0495	171	1111	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.506	137	1111	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:49:48,504] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11411/tc_result.tsv
[2023-03-17 23:49:48,505] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:49:48,505] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:49:48,505] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/checkm_data
[2023-03-17 23:49:48,505] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:49:48,515] [INFO] Task started: CheckM
[2023-03-17 23:49:48,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11411/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11411/checkm_input OceanDNA-b11411/checkm_result
[2023-03-17 23:50:41,899] [INFO] Task succeeded: CheckM
[2023-03-17 23:50:41,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:50:41,902] [INFO] ===== Completeness check finished =====
[2023-03-17 23:50:41,902] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:50:41,902] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11411/markers.fasta)
[2023-03-17 23:50:41,902] [INFO] Task started: Blastn
[2023-03-17 23:50:41,903] [INFO] Running command: blastn -query OceanDNA-b11411/markers.fasta -db /var/lib/cwl/stg20efdce0-5a8f-4011-8813-cdb5dda5adc1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11411/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:50:42,854] [INFO] Task succeeded: Blastn
[2023-03-17 23:50:42,855] [INFO] Selected 20 target genomes.
[2023-03-17 23:50:42,855] [INFO] Target genome list was writen to OceanDNA-b11411/target_genomes_gtdb.txt
[2023-03-17 23:50:42,866] [INFO] Task started: fastANI
[2023-03-17 23:50:42,866] [INFO] Running command: fastANI --query /var/lib/cwl/stgabb15b97-a449-44fc-845c-4d0eef3132dd/OceanDNA-b11411.fa --refList OceanDNA-b11411/target_genomes_gtdb.txt --output OceanDNA-b11411/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:50:56,258] [INFO] Task succeeded: fastANI
[2023-03-17 23:50:56,269] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:50:56,269] [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_013213835.1	s__Winogradskyella sp013213835	99.7864	1070	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002722255.1	s__Winogradskyella sp002722255	78.8855	356	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	99.90	99.90	0.80	0.80	2	-
GCF_014297365.1	s__Winogradskyella echinorum	78.7418	392	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005869935.1	s__Winogradskyella algicola	78.6479	425	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971725.1	s__Winogradskyella sp001971725	78.499	373	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000171875.1	s__Winogradskyella sp000171875	78.49	372	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014243395.1	s__Winogradskyella flava	78.4024	347	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002682935.1	s__Winogradskyella sp002682935	78.3794	406	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019203985.1	s__Winogradskyella sp019203985	78.3709	363	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744625.1	s__Winogradskyella sp016744625	78.2263	377	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003387355.1	s__Winogradskyella sediminis	78.221	315	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.63	98.63	0.93	0.93	2	-
GCF_009741275.1	s__Winogradskyella endarachnes	78.1903	357	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860565.1	s__Winogradskyella psychrotolerans_B	78.1493	336	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000828715.1	s__Winogradskyella sp000828715	78.1218	410	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364335.1	s__Winogradskyella sp002364335	78.1002	327	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013404085.1	s__Winogradskyella helgolandensis	78.0626	334	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	98.14	98.14	0.94	0.94	2	-
GCF_013403955.1	s__Winogradskyella vidalii	77.937	298	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004366715.1	s__Meridianimaribacter flavus	77.8465	255	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Meridianimaribacter	95.0	97.44	97.06	0.91	0.87	3	-
GCF_018860825.1	s__Oceanihabitans sp018860825	77.5503	242	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162685.1	s__Psychroserpens sp002162685	77.4737	250	1111	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:50:56,272] [INFO] GTDB search result was written to OceanDNA-b11411/result_gtdb.tsv
[2023-03-17 23:50:56,272] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:50:56,276] [INFO] DFAST_QC result json was written to OceanDNA-b11411/dqc_result.json
[2023-03-17 23:50:56,276] [INFO] DFAST_QC completed!
[2023-03-17 23:50:56,276] [INFO] Total running time: 0h1m46s