[2023-06-08 16:47:59,043] [INFO] DFAST_QC pipeline started.
[2023-06-08 16:47:59,045] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 16:47:59,045] [INFO] DQC Reference Directory: /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference
[2023-06-08 16:48:00,324] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 16:48:00,325] [INFO] Task started: Prodigal
[2023-06-08 16:48:00,325] [INFO] Running command: gunzip -c /var/lib/cwl/stg340160cc-4a12-4bc4-977a-30d0b2f72b67/GCA_945862035.1_ME-08apr19-328_genomic.fna.gz | prodigal -d GCA_945862035.1_ME-08apr19-328_genomic.fna/cds.fna -a GCA_945862035.1_ME-08apr19-328_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 16:48:15,670] [INFO] Task succeeded: Prodigal
[2023-06-08 16:48:15,671] [INFO] Task started: HMMsearch
[2023-06-08 16:48:15,671] [INFO] Running command: hmmsearch --tblout GCA_945862035.1_ME-08apr19-328_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/reference_markers.hmm GCA_945862035.1_ME-08apr19-328_genomic.fna/protein.faa > /dev/null
[2023-06-08 16:48:15,943] [INFO] Task succeeded: HMMsearch
[2023-06-08 16:48:15,944] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg340160cc-4a12-4bc4-977a-30d0b2f72b67/GCA_945862035.1_ME-08apr19-328_genomic.fna.gz]
[2023-06-08 16:48:15,979] [INFO] Query marker FASTA was written to GCA_945862035.1_ME-08apr19-328_genomic.fna/markers.fasta
[2023-06-08 16:48:15,980] [INFO] Task started: Blastn
[2023-06-08 16:48:15,980] [INFO] Running command: blastn -query GCA_945862035.1_ME-08apr19-328_genomic.fna/markers.fasta -db /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/reference_markers.fasta -out GCA_945862035.1_ME-08apr19-328_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:48:16,699] [INFO] Task succeeded: Blastn
[2023-06-08 16:48:16,705] [INFO] Selected 17 target genomes.
[2023-06-08 16:48:16,705] [INFO] Target genome list was writen to GCA_945862035.1_ME-08apr19-328_genomic.fna/target_genomes.txt
[2023-06-08 16:48:16,707] [INFO] Task started: fastANI
[2023-06-08 16:48:16,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg340160cc-4a12-4bc4-977a-30d0b2f72b67/GCA_945862035.1_ME-08apr19-328_genomic.fna.gz --refList GCA_945862035.1_ME-08apr19-328_genomic.fna/target_genomes.txt --output GCA_945862035.1_ME-08apr19-328_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 16:48:30,348] [INFO] Task succeeded: fastANI
[2023-06-08 16:48:30,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 16:48:30,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 16:48:30,358] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 16:48:30,358] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 16:48:30,358] [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	77.8471	152	802	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.4225	91	802	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.3935	150	802	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.2167	146	802	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.9381	99	802	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.889	94	802	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.7574	75	802	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7563	76	802	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 16:48:30,360] [INFO] DFAST Taxonomy check result was written to GCA_945862035.1_ME-08apr19-328_genomic.fna/tc_result.tsv
[2023-06-08 16:48:30,361] [INFO] ===== Taxonomy check completed =====
[2023-06-08 16:48:30,361] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 16:48:30,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/checkm_data
[2023-06-08 16:48:30,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 16:48:30,394] [INFO] Task started: CheckM
[2023-06-08 16:48:30,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945862035.1_ME-08apr19-328_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945862035.1_ME-08apr19-328_genomic.fna/checkm_input GCA_945862035.1_ME-08apr19-328_genomic.fna/checkm_result
[2023-06-08 16:49:15,142] [INFO] Task succeeded: CheckM
[2023-06-08 16:49:15,144] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.42%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 16:49:15,166] [INFO] ===== Completeness check finished =====
[2023-06-08 16:49:15,167] [INFO] ===== Start GTDB Search =====
[2023-06-08 16:49:15,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945862035.1_ME-08apr19-328_genomic.fna/markers.fasta)
[2023-06-08 16:49:15,168] [INFO] Task started: Blastn
[2023-06-08 16:49:15,168] [INFO] Running command: blastn -query GCA_945862035.1_ME-08apr19-328_genomic.fna/markers.fasta -db /var/lib/cwl/stg575e1c9e-4df0-48d9-81fb-abc7a249b90e/dqc_reference/reference_markers_gtdb.fasta -out GCA_945862035.1_ME-08apr19-328_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 16:49:16,109] [INFO] Task succeeded: Blastn
[2023-06-08 16:49:16,114] [INFO] Selected 20 target genomes.
[2023-06-08 16:49:16,114] [INFO] Target genome list was writen to GCA_945862035.1_ME-08apr19-328_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 16:49:16,115] [INFO] Task started: fastANI
[2023-06-08 16:49:16,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg340160cc-4a12-4bc4-977a-30d0b2f72b67/GCA_945862035.1_ME-08apr19-328_genomic.fna.gz --refList GCA_945862035.1_ME-08apr19-328_genomic.fna/target_genomes_gtdb.txt --output GCA_945862035.1_ME-08apr19-328_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 16:49:30,123] [INFO] Task succeeded: fastANI
[2023-06-08 16:49:30,145] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 16:49:30,146] [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_903825285.1	s__Opi-474 sp903825285	78.8279	178	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.78	99.55	0.96	0.94	12	-
GCA_018239845.1	s__Opitutus sp018239845	78.5836	199	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	78.3203	181	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830425.1	s__Opi-474 sp903830425	78.2488	182	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_018239675.1	s__Opi-474 sp018239675	78.2281	181	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862595.1	s__UBA6669 sp903862595	78.112	140	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCA_016187925.1	s__Didemnitutus sp016187925	78.0076	159	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001746835.1	s__Lacunisphaera limnophila	77.9857	183	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217595.1	s__MWDT01 sp016217595	77.9666	98	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903876795.1	s__Rariglobus sp903876795	77.9444	165	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559335.1	s__Rariglobus hedericola	77.8518	151	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877135.1	s__Opitutus sp903877135	77.8392	143	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_016871755.1	s__UBA6669 sp016871755	77.8055	191	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	77.7501	172	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873805.1	s__CAIQQB01 sp903873805	77.7284	171	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIQQB01	95.0	99.97	99.97	0.95	0.95	2	-
GCA_000972765.1	s__IMCC26134_A sp000972765	77.7149	129	802	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_903881475.1	s__Opi-474 sp903881475	77.6926	179	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_903948415.1	s__CAITWF01 sp903948415	77.5707	162	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879845.1	s__J108 sp014879845	77.2612	137	802	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002343915.1	s__Nannocystis exedens	74.7526	76	802	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-08 16:49:30,148] [INFO] GTDB search result was written to GCA_945862035.1_ME-08apr19-328_genomic.fna/result_gtdb.tsv
[2023-06-08 16:49:30,148] [INFO] ===== GTDB Search completed =====
[2023-06-08 16:49:30,172] [INFO] DFAST_QC result json was written to GCA_945862035.1_ME-08apr19-328_genomic.fna/dqc_result.json
[2023-06-08 16:49:30,172] [INFO] DFAST_QC completed!
[2023-06-08 16:49:30,172] [INFO] Total running time: 0h1m31s