[2023-03-18 00:21:56,079] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:21:56,079] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:21:56,079] [INFO] DQC Reference Directory: /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference
[2023-03-18 00:21:57,172] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:21:57,172] [INFO] Task started: Prodigal
[2023-03-18 00:21:57,172] [INFO] Running command: cat /var/lib/cwl/stg244ce137-d3e9-445d-b8e8-3a1faf997d05/OceanDNA-b6289.fa | prodigal -d OceanDNA-b6289/cds.fna -a OceanDNA-b6289/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:22:15,060] [INFO] Task succeeded: Prodigal
[2023-03-18 00:22:15,060] [INFO] Task started: HMMsearch
[2023-03-18 00:22:15,060] [INFO] Running command: hmmsearch --tblout OceanDNA-b6289/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/reference_markers.hmm OceanDNA-b6289/protein.faa > /dev/null
[2023-03-18 00:22:15,267] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:22:15,268] [INFO] Found 6/6 markers.
[2023-03-18 00:22:15,286] [INFO] Query marker FASTA was written to OceanDNA-b6289/markers.fasta
[2023-03-18 00:22:15,287] [INFO] Task started: Blastn
[2023-03-18 00:22:15,287] [INFO] Running command: blastn -query OceanDNA-b6289/markers.fasta -db /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/reference_markers.fasta -out OceanDNA-b6289/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:22:15,902] [INFO] Task succeeded: Blastn
[2023-03-18 00:22:15,904] [INFO] Selected 25 target genomes.
[2023-03-18 00:22:15,904] [INFO] Target genome list was writen to OceanDNA-b6289/target_genomes.txt
[2023-03-18 00:22:15,918] [INFO] Task started: fastANI
[2023-03-18 00:22:15,918] [INFO] Running command: fastANI --query /var/lib/cwl/stg244ce137-d3e9-445d-b8e8-3a1faf997d05/OceanDNA-b6289.fa --refList OceanDNA-b6289/target_genomes.txt --output OceanDNA-b6289/fastani_result.tsv --threads 1
[2023-03-18 00:22:30,424] [INFO] Task succeeded: fastANI
[2023-03-18 00:22:30,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:22:30,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:22:30,439] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:22:30,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:22:30,439] [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
Pontimicrobium aquaticum	strain=CAU 1491	GCA_005047595.1	2565367	2565367	type	True	81.0527	610	918	95	below_threshold
Seonamhaeicola algicola	strain=Gy8	GCA_007997385.1	1719036	1719036	type	True	77.6322	200	918	95	below_threshold
Lacinutrix himadriensis	strain=E4-9a	GCA_001418105.1	641549	641549	type	True	77.5495	237	918	95	below_threshold
Algibacter marinivivus	strain=ZY111	GCA_003143755.1	2100723	2100723	type	True	77.5213	216	918	95	below_threshold
Seonamhaeicola maritimus	strain=1505	GCA_008056315.1	2591822	2591822	type	True	77.5168	210	918	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.5047	210	918	95	below_threshold
Tamlana haliotis	strain=B1N29	GCA_008806375.1	2614804	2614804	type	True	77.4958	151	918	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.4955	197	918	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4863	220	918	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014284085.1	538189	538189	type	True	77.4767	214	918	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.4745	216	918	95	below_threshold
Winogradskyella echinorum	strain=KCTC 22026	GCA_014297365.1	538189	538189	type	True	77.4628	215	918	95	below_threshold
Seonamhaeicola aphaedonensis	strain=CECT 8487	GCA_003386195.1	1461338	1461338	type	True	77.4626	150	918	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.4332	219	918	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.4269	203	918	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.3965	177	918	95	below_threshold
Formosa algae	strain=KMM 3553	GCA_001439665.1	225843	225843	type	True	77.3836	163	918	95	below_threshold
Psychroserpens mesophilus	strain=JCM 13413	GCA_000826645.1	325473	325473	type	True	77.3711	206	918	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.3663	202	918	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.3086	186	918	95	below_threshold
Hanstruepera neustonica	strain=JCM19743	GCA_002895005.1	1445657	1445657	type	True	77.2306	170	918	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.2215	224	918	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.0455	167	918	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.0135	158	918	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.9746	159	918	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:22:30,440] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6289/tc_result.tsv
[2023-03-18 00:22:30,440] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:22:30,440] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:22:30,440] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/checkm_data
[2023-03-18 00:22:30,441] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:22:30,445] [INFO] Task started: CheckM
[2023-03-18 00:22:30,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6289/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6289/checkm_input OceanDNA-b6289/checkm_result
[2023-03-18 00:23:16,974] [INFO] Task succeeded: CheckM
[2023-03-18 00:23:16,974] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:23:16,976] [INFO] ===== Completeness check finished =====
[2023-03-18 00:23:16,976] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:23:16,977] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6289/markers.fasta)
[2023-03-18 00:23:16,977] [INFO] Task started: Blastn
[2023-03-18 00:23:16,977] [INFO] Running command: blastn -query OceanDNA-b6289/markers.fasta -db /var/lib/cwl/stga68b7a60-7751-4f70-acc0-d405f0f9cbef/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6289/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:23:17,889] [INFO] Task succeeded: Blastn
[2023-03-18 00:23:17,889] [INFO] Selected 18 target genomes.
[2023-03-18 00:23:17,889] [INFO] Target genome list was writen to OceanDNA-b6289/target_genomes_gtdb.txt
[2023-03-18 00:23:17,908] [INFO] Task started: fastANI
[2023-03-18 00:23:17,908] [INFO] Running command: fastANI --query /var/lib/cwl/stg244ce137-d3e9-445d-b8e8-3a1faf997d05/OceanDNA-b6289.fa --refList OceanDNA-b6289/target_genomes_gtdb.txt --output OceanDNA-b6289/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:23:28,092] [INFO] Task succeeded: fastANI
[2023-03-18 00:23:28,102] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:23:28,102] [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_011777505.1	s__CAU-1491 sp011777505	81.9538	672	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005047595.1	s__CAU-1491 sp005047595	81.0634	609	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__CAU-1491	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151975.1	s__PRS1 sp013151975	78.7986	305	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	78.0388	273	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003650305.1	s__PRS1 sp003650305	77.897	294	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	77.7249	285	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002741945.1	s__Wocania sp002741945	77.6976	249	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012931685.1	s__Pseudobizionia ponticola	77.6376	185	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudobizionia	95.0	97.35	97.35	0.92	0.92	2	-
GCF_001971785.1	s__Seonamhaeicola sp001971785	77.5552	231	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003143755.1	s__Algibacter_B sp003143755	77.5213	216	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008056315.1	s__Seonamhaeicola maritimus	77.5168	210	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641635.1	s__Aquaticitalea lipolytica	77.4853	268	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aquaticitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003709165.1	s__PRS1 sp003709165	77.43	212	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__PRS1	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000826645.1	s__Psychroserpens mesophilus	77.3733	205	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213835.1	s__Winogradskyella sp013213835	77.3077	172	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Winogradskyella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013215095.1	s__DT-34 sp013215095	77.1469	189	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480415.1	s__Algibacter_B sp905480415	77.1179	185	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425305.1	s__Psychroserpens burtonensis	76.8723	190	918	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Psychroserpens	95.0	99.48	99.48	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-18 00:23:28,102] [INFO] GTDB search result was written to OceanDNA-b6289/result_gtdb.tsv
[2023-03-18 00:23:28,102] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:23:28,104] [INFO] DFAST_QC result json was written to OceanDNA-b6289/dqc_result.json
[2023-03-18 00:23:28,105] [INFO] DFAST_QC completed!
[2023-03-18 00:23:28,105] [INFO] Total running time: 0h1m32s