[2023-06-08 01:48:49,695] [INFO] DFAST_QC pipeline started.
[2023-06-08 01:48:49,697] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 01:48:49,697] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference
[2023-06-08 01:48:50,929] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 01:48:50,930] [INFO] Task started: Prodigal
[2023-06-08 01:48:50,931] [INFO] Running command: gunzip -c /var/lib/cwl/stg97c3f9cc-ffda-4ae9-9db8-e396087ada42/GCA_945874545.1_MiE-14oct19-92_genomic.fna.gz | prodigal -d GCA_945874545.1_MiE-14oct19-92_genomic.fna/cds.fna -a GCA_945874545.1_MiE-14oct19-92_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 01:49:11,496] [INFO] Task succeeded: Prodigal
[2023-06-08 01:49:11,497] [INFO] Task started: HMMsearch
[2023-06-08 01:49:11,497] [INFO] Running command: hmmsearch --tblout GCA_945874545.1_MiE-14oct19-92_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/reference_markers.hmm GCA_945874545.1_MiE-14oct19-92_genomic.fna/protein.faa > /dev/null
[2023-06-08 01:49:11,733] [INFO] Task succeeded: HMMsearch
[2023-06-08 01:49:11,735] [INFO] Found 6/6 markers.
[2023-06-08 01:49:11,779] [INFO] Query marker FASTA was written to GCA_945874545.1_MiE-14oct19-92_genomic.fna/markers.fasta
[2023-06-08 01:49:11,779] [INFO] Task started: Blastn
[2023-06-08 01:49:11,780] [INFO] Running command: blastn -query GCA_945874545.1_MiE-14oct19-92_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/reference_markers.fasta -out GCA_945874545.1_MiE-14oct19-92_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:49:12,406] [INFO] Task succeeded: Blastn
[2023-06-08 01:49:12,412] [INFO] Selected 12 target genomes.
[2023-06-08 01:49:12,413] [INFO] Target genome list was writen to GCA_945874545.1_MiE-14oct19-92_genomic.fna/target_genomes.txt
[2023-06-08 01:49:12,414] [INFO] Task started: fastANI
[2023-06-08 01:49:12,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c3f9cc-ffda-4ae9-9db8-e396087ada42/GCA_945874545.1_MiE-14oct19-92_genomic.fna.gz --refList GCA_945874545.1_MiE-14oct19-92_genomic.fna/target_genomes.txt --output GCA_945874545.1_MiE-14oct19-92_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 01:49:20,626] [INFO] Task succeeded: fastANI
[2023-06-08 01:49:20,626] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 01:49:20,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 01:49:20,642] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 01:49:20,642] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 01:49:20,642] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.8991	236	1121	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.4584	114	1121	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.155	216	1121	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	77.1466	75	1121	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.0871	233	1121	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.9026	159	1121	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	76.3699	185	1121	95	below_threshold
Bosea caraganae	strain=RCAM 04680	GCA_003351345.1	2763117	2763117	type	True	74.8832	97	1121	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	74.7474	68	1121	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	74.7436	69	1121	95	below_threshold
Actinoplanes tereljensis	strain=NBRC 105297	GCA_016862435.1	571912	571912	type	True	74.7384	166	1121	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 01:49:20,644] [INFO] DFAST Taxonomy check result was written to GCA_945874545.1_MiE-14oct19-92_genomic.fna/tc_result.tsv
[2023-06-08 01:49:20,645] [INFO] ===== Taxonomy check completed =====
[2023-06-08 01:49:20,645] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 01:49:20,645] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/checkm_data
[2023-06-08 01:49:20,646] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 01:49:20,684] [INFO] Task started: CheckM
[2023-06-08 01:49:20,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945874545.1_MiE-14oct19-92_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945874545.1_MiE-14oct19-92_genomic.fna/checkm_input GCA_945874545.1_MiE-14oct19-92_genomic.fna/checkm_result
[2023-06-08 01:50:15,640] [INFO] Task succeeded: CheckM
[2023-06-08 01:50:15,641] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 76.39%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 01:50:15,662] [INFO] ===== Completeness check finished =====
[2023-06-08 01:50:15,663] [INFO] ===== Start GTDB Search =====
[2023-06-08 01:50:15,663] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945874545.1_MiE-14oct19-92_genomic.fna/markers.fasta)
[2023-06-08 01:50:15,664] [INFO] Task started: Blastn
[2023-06-08 01:50:15,664] [INFO] Running command: blastn -query GCA_945874545.1_MiE-14oct19-92_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9f5b50f-7586-4c16-8fba-60943e736a6e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945874545.1_MiE-14oct19-92_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 01:50:16,625] [INFO] Task succeeded: Blastn
[2023-06-08 01:50:16,629] [INFO] Selected 15 target genomes.
[2023-06-08 01:50:16,630] [INFO] Target genome list was writen to GCA_945874545.1_MiE-14oct19-92_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 01:50:16,639] [INFO] Task started: fastANI
[2023-06-08 01:50:16,639] [INFO] Running command: fastANI --query /var/lib/cwl/stg97c3f9cc-ffda-4ae9-9db8-e396087ada42/GCA_945874545.1_MiE-14oct19-92_genomic.fna.gz --refList GCA_945874545.1_MiE-14oct19-92_genomic.fna/target_genomes_gtdb.txt --output GCA_945874545.1_MiE-14oct19-92_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 01:50:27,746] [INFO] Task succeeded: fastANI
[2023-06-08 01:50:27,764] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 01:50:27,765] [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_903869675.1	s__IMCC26134_A sp903869675	82.8263	531	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	99.95	99.94	0.98	0.98	3	-
GCA_010027235.1	s__IMCC26134_A sp010027235	81.9241	399	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000972765.1	s__IMCC26134_A sp000972765	79.7016	353	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	99.41	99.35	0.95	0.94	9	-
GCA_903876795.1	s__Rariglobus sp903876795	78.9122	301	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904685.1	s__Rariglobus sp903904685	78.0619	190	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.84	99.84	0.96	0.96	2	-
GCF_007559335.1	s__Rariglobus hedericola	77.9129	235	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382525.1	s__Rariglobus sp002382525	77.8375	210	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	99.24	99.24	0.83	0.83	2	-
GCA_000242935.3	s__Geminisphaera sp000242935	77.6681	307	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_903872505.1	s__Opi-474 sp903872505	77.4179	220	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903929355.1	s__CAIYUN01 sp903929355	77.2358	221	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYUN01	95.0	99.96	99.94	0.97	0.97	4	-
GCF_000171235.2	s__Geminisphaera colitermitum	77.1669	215	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	97.34	97.31	0.79	0.79	3	-
GCA_001650175.1	s__Ereboglobus sp001650175	77.125	312	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288455.1	s__ER46 sp002288455	76.9834	241	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822585.1	s__Didemnitutus sp013822585	76.9789	155	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	76.9611	235	1121	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 01:50:27,767] [INFO] GTDB search result was written to GCA_945874545.1_MiE-14oct19-92_genomic.fna/result_gtdb.tsv
[2023-06-08 01:50:27,767] [INFO] ===== GTDB Search completed =====
[2023-06-08 01:50:27,771] [INFO] DFAST_QC result json was written to GCA_945874545.1_MiE-14oct19-92_genomic.fna/dqc_result.json
[2023-06-08 01:50:27,771] [INFO] DFAST_QC completed!
[2023-06-08 01:50:27,771] [INFO] Total running time: 0h1m38s