[2023-03-17 00:02:20,757] [INFO] DFAST_QC pipeline started.
[2023-03-17 00:02:20,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 00:02:20,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference
[2023-03-17 00:02:21,885] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 00:02:21,885] [INFO] Task started: Prodigal
[2023-03-17 00:02:21,885] [INFO] Running command: cat /var/lib/cwl/stgd04b52f8-d562-4e4e-873d-519d9387ee51/OceanDNA-b36154.fa | prodigal -d OceanDNA-b36154/cds.fna -a OceanDNA-b36154/protein.faa -g 11 -q > /dev/null
[2023-03-17 00:02:37,421] [INFO] Task succeeded: Prodigal
[2023-03-17 00:02:37,422] [INFO] Task started: HMMsearch
[2023-03-17 00:02:37,422] [INFO] Running command: hmmsearch --tblout OceanDNA-b36154/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/reference_markers.hmm OceanDNA-b36154/protein.faa > /dev/null
[2023-03-17 00:02:37,616] [INFO] Task succeeded: HMMsearch
[2023-03-17 00:02:37,617] [INFO] Found 6/6 markers.
[2023-03-17 00:02:37,636] [INFO] Query marker FASTA was written to OceanDNA-b36154/markers.fasta
[2023-03-17 00:02:37,637] [INFO] Task started: Blastn
[2023-03-17 00:02:37,637] [INFO] Running command: blastn -query OceanDNA-b36154/markers.fasta -db /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/reference_markers.fasta -out OceanDNA-b36154/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:02:38,375] [INFO] Task succeeded: Blastn
[2023-03-17 00:02:38,376] [INFO] Selected 22 target genomes.
[2023-03-17 00:02:38,377] [INFO] Target genome list was writen to OceanDNA-b36154/target_genomes.txt
[2023-03-17 00:02:38,575] [INFO] Task started: fastANI
[2023-03-17 00:02:38,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04b52f8-d562-4e4e-873d-519d9387ee51/OceanDNA-b36154.fa --refList OceanDNA-b36154/target_genomes.txt --output OceanDNA-b36154/fastani_result.tsv --threads 1
[2023-03-17 00:02:51,918] [INFO] Task succeeded: fastANI
[2023-03-17 00:02:51,918] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 00:02:51,918] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 00:02:51,929] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 00:02:51,929] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 00:02:51,929] [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
Salinisphaera shabanensis	strain=E1L3A	GCA_000215955.3	180542	180542	type	True	81.0683	526	826	95	below_threshold
Salinisphaera halophila	strain=YIM 95161	GCA_003732545.1	1304158	1304158	type	True	81.0523	519	826	95	below_threshold
Salinisphaera orenii	strain=MK-B5	GCA_003788635.1	856731	856731	type	True	80.8576	520	826	95	below_threshold
Salinisphaera japonica	strain=YTM-1	GCA_003788585.1	1304270	1304270	type	True	78.1372	259	826	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	76.3163	85	826	95	below_threshold
Alcanivorax mobilis	strain=MT13131	GCA_002864685.1	2019569	2019569	type	True	76.1532	69	826	95	below_threshold
Alcanivorax venustensis	strain=ISO4	GCA_015356855.1	172371	172371	type	True	76.0518	84	826	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	75.9296	78	826	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	75.9112	96	826	95	below_threshold
Metallibacterium scheffleri	strain=DSM 24874	GCA_004798955.1	993689	993689	type	True	75.9111	62	826	95	below_threshold
Metallibacterium scheffleri	strain=DKE6	GCA_002077135.1	993689	993689	type	True	75.9111	62	826	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	75.8753	79	826	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.8171	121	826	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	75.6695	76	826	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	75.6392	76	826	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	75.6376	78	826	95	below_threshold
Chromohalobacter sarecensis	strain=DSM 15547	GCA_023061135.1	245294	245294	type	True	75.5975	53	826	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	75.4641	92	826	95	below_threshold
Marinobacterium arenosum	strain=CAU 1594	GCA_019795155.1	2862496	2862496	type	True	75.4544	64	826	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 00:02:51,950] [INFO] DFAST Taxonomy check result was written to OceanDNA-b36154/tc_result.tsv
[2023-03-17 00:02:52,000] [INFO] ===== Taxonomy check completed =====
[2023-03-17 00:02:52,000] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 00:02:52,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/checkm_data
[2023-03-17 00:02:52,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 00:02:52,006] [INFO] Task started: CheckM
[2023-03-17 00:02:52,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b36154/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b36154/checkm_input OceanDNA-b36154/checkm_result
[2023-03-17 00:03:32,532] [INFO] Task succeeded: CheckM
[2023-03-17 00:03:32,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 00:03:32,577] [INFO] ===== Completeness check finished =====
[2023-03-17 00:03:32,578] [INFO] ===== Start GTDB Search =====
[2023-03-17 00:03:32,578] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b36154/markers.fasta)
[2023-03-17 00:03:32,579] [INFO] Task started: Blastn
[2023-03-17 00:03:32,579] [INFO] Running command: blastn -query OceanDNA-b36154/markers.fasta -db /var/lib/cwl/stg6ff16dcf-849c-4436-8b38-bbdcd1b52664/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b36154/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 00:03:33,931] [INFO] Task succeeded: Blastn
[2023-03-17 00:03:33,932] [INFO] Selected 12 target genomes.
[2023-03-17 00:03:33,932] [INFO] Target genome list was writen to OceanDNA-b36154/target_genomes_gtdb.txt
[2023-03-17 00:03:34,162] [INFO] Task started: fastANI
[2023-03-17 00:03:34,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgd04b52f8-d562-4e4e-873d-519d9387ee51/OceanDNA-b36154.fa --refList OceanDNA-b36154/target_genomes_gtdb.txt --output OceanDNA-b36154/fastani_result_gtdb.tsv --threads 1
[2023-03-17 00:03:42,002] [INFO] Task succeeded: fastANI
[2023-03-17 00:03:42,009] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 00:03:42,009] [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_017744135.1	s__Salinisphaera sp017744135	97.0411	779	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002729955.1	s__Salinisphaera sp002729955	81.6055	556	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002433465.1	s__Salinisphaera sp002433465	81.2081	478	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215955.2	s__Salinisphaera shabanensis	81.1063	523	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003732545.1	s__Salinisphaera halophila	81.0447	520	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003788635.1	s__Salinisphaera orenii	80.8576	520	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	96.8739	N/A	N/A	N/A	N/A	1	-
GCF_003177035.1	s__Salinisphaera sp003177035	78.3556	324	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002715985.1	s__Salinisphaera sp002715985	77.9477	191	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Nevskiales;f__Salinisphaeraceae;g__Salinisphaera	95.0	99.39	99.39	0.77	0.77	2	-
GCF_000377905.1	s__Thioalkalivibrio sp000377905	76.4165	54	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932505.1	s__Thiohalobacter thiocyanaticus	75.9296	78	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002077135.1	s__Metallibacterium scheffleri	75.9111	62	826	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Metallibacterium	95.0	98.26	96.51	0.97	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-17 00:03:42,009] [INFO] GTDB search result was written to OceanDNA-b36154/result_gtdb.tsv
[2023-03-17 00:03:42,009] [INFO] ===== GTDB Search completed =====
[2023-03-17 00:03:42,018] [INFO] DFAST_QC result json was written to OceanDNA-b36154/dqc_result.json
[2023-03-17 00:03:42,018] [INFO] DFAST_QC completed!
[2023-03-17 00:03:42,018] [INFO] Total running time: 0h1m21s