[2023-06-28 02:21:49,761] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:49,763] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:49,763] [INFO] DQC Reference Directory: /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference
[2023-06-28 02:21:51,227] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:51,228] [INFO] Task started: Prodigal
[2023-06-28 02:21:51,228] [INFO] Running command: gunzip -c /var/lib/cwl/stgf115b084-7269-486e-bbb0-49b935b30202/GCA_944382985.1_BRZ_EH_bin149_genomic.fna.gz | prodigal -d GCA_944382985.1_BRZ_EH_bin149_genomic.fna/cds.fna -a GCA_944382985.1_BRZ_EH_bin149_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:21:57,417] [INFO] Task succeeded: Prodigal
[2023-06-28 02:21:57,418] [INFO] Task started: HMMsearch
[2023-06-28 02:21:57,418] [INFO] Running command: hmmsearch --tblout GCA_944382985.1_BRZ_EH_bin149_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/reference_markers.hmm GCA_944382985.1_BRZ_EH_bin149_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:21:57,686] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:21:57,689] [INFO] Found 6/6 markers.
[2023-06-28 02:21:57,713] [INFO] Query marker FASTA was written to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/markers.fasta
[2023-06-28 02:21:57,714] [INFO] Task started: Blastn
[2023-06-28 02:21:57,714] [INFO] Running command: blastn -query GCA_944382985.1_BRZ_EH_bin149_genomic.fna/markers.fasta -db /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/reference_markers.fasta -out GCA_944382985.1_BRZ_EH_bin149_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:21:58,335] [INFO] Task succeeded: Blastn
[2023-06-28 02:21:58,340] [INFO] Selected 13 target genomes.
[2023-06-28 02:21:58,340] [INFO] Target genome list was writen to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/target_genomes.txt
[2023-06-28 02:21:58,341] [INFO] Task started: fastANI
[2023-06-28 02:21:58,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgf115b084-7269-486e-bbb0-49b935b30202/GCA_944382985.1_BRZ_EH_bin149_genomic.fna.gz --refList GCA_944382985.1_BRZ_EH_bin149_genomic.fna/target_genomes.txt --output GCA_944382985.1_BRZ_EH_bin149_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:22:05,454] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:05,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:22:05,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:22:05,466] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:22:05,466] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 02:22:05,466] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	78.5058	246	688	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	78.3537	188	688	95	below_threshold
Clostridium phoceensis	strain=GD3	GCA_001244495.1	1650661	1650661	type	True	78.2762	172	688	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	78.1549	178	688	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	78.1098	163	688	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	78.0476	207	688	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.772	130	688	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.7141	146	688	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	77.4061	112	688	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.4057	128	688	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.9605	91	688	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	76.7477	75	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 02:22:05,468] [INFO] DFAST Taxonomy check result was written to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/tc_result.tsv
[2023-06-28 02:22:05,469] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:22:05,469] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:22:05,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/checkm_data
[2023-06-28 02:22:05,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:22:05,515] [INFO] Task started: CheckM
[2023-06-28 02:22:05,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944382985.1_BRZ_EH_bin149_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944382985.1_BRZ_EH_bin149_genomic.fna/checkm_input GCA_944382985.1_BRZ_EH_bin149_genomic.fna/checkm_result
[2023-06-28 02:22:29,570] [INFO] Task succeeded: CheckM
[2023-06-28 02:22:29,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:22:29,598] [INFO] ===== Completeness check finished =====
[2023-06-28 02:22:29,599] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:22:29,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944382985.1_BRZ_EH_bin149_genomic.fna/markers.fasta)
[2023-06-28 02:22:29,599] [INFO] Task started: Blastn
[2023-06-28 02:22:29,600] [INFO] Running command: blastn -query GCA_944382985.1_BRZ_EH_bin149_genomic.fna/markers.fasta -db /var/lib/cwl/stg71d7aaf6-2d73-4c77-aedd-d13c16eccccb/dqc_reference/reference_markers_gtdb.fasta -out GCA_944382985.1_BRZ_EH_bin149_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:30,634] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:30,639] [INFO] Selected 26 target genomes.
[2023-06-28 02:22:30,640] [INFO] Target genome list was writen to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:22:30,673] [INFO] Task started: fastANI
[2023-06-28 02:22:30,673] [INFO] Running command: fastANI --query /var/lib/cwl/stgf115b084-7269-486e-bbb0-49b935b30202/GCA_944382985.1_BRZ_EH_bin149_genomic.fna.gz --refList GCA_944382985.1_BRZ_EH_bin149_genomic.fna/target_genomes_gtdb.txt --output GCA_944382985.1_BRZ_EH_bin149_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:22:42,657] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:42,681] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 02:22:42,681] [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_904420435.1	s__CAJFPI01 sp904420435	98.3271	568	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_904419145.1	s__CAJFPI01 sp904419145	81.3376	339	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	98.67	98.54	0.90	0.87	4	-
GCA_904398675.1	s__CAJFPI01 sp904398675	80.9316	290	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420145.1	s__CAJFPI01 sp904420145	80.9137	327	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAJFPI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712665.1	s__Pelethomonas intestinigallinarum	80.7789	261	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	97.99	97.70	0.89	0.81	4	-
GCA_910579965.1	s__Pelethomonas sp910579965	80.0228	267	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118505.1	s__Dysosmobacter excrementavium	79.8736	266	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577915.1	s__Pelethomonas sp910577915	79.85	267	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	79.7197	272	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	79.715	244	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_910579485.1	s__Pelethomonas sp910579485	79.2737	228	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014237695.1	s__Pelethomonas sp014237695	79.1274	145	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Pelethomonas	95.0	97.53	97.53	0.82	0.82	2	-
GCA_904420465.1	s__Lawsonibacter sp904420465	78.8118	177	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587875.1	s__Dysosmobacter sp910587875	78.5717	199	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005121165.2	s__Dysosmobacter welbionis	78.5548	241	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCA_018711785.1	s__Galloscillospira_A excrementavium	78.343	163	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	98.56	98.56	0.94	0.94	2	-
GCF_014287875.1	s__Lawsonibacter sp014287875	78.3373	148	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.47	96.91	0.89	0.83	4	-
GCF_003478995.1	s__Lawsonibacter sp003478995	78.2042	156	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_910583785.1	s__Dysosmobacter sp910583785	78.204	184	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549405.1	s__Lawsonibacter sp900549405	78.0613	142	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	97.96	97.96	0.89	0.89	2	-
GCF_002161175.1	s__Lawsonibacter sp002161175	78.0233	140	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900553135.1	s__Lawsonibacter sp900553135	78.0129	145	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715695.1	s__Galloscillospira_A stercoripullorum	77.882	149	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Galloscillospira_A	95.0	99.04	99.04	0.82	0.82	2	-
GCA_905205085.1	s__Lawsonibacter sp900766145	77.8387	141	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Lawsonibacter	95.0	99.79	99.79	0.87	0.87	2	-
GCA_910578935.1	s__Dysosmobacter sp910578935	77.6108	140	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584995.1	s__Dysosmobacter sp910584995	77.5929	152	688	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:22:42,684] [INFO] GTDB search result was written to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/result_gtdb.tsv
[2023-06-28 02:22:42,684] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:22:42,692] [INFO] DFAST_QC result json was written to GCA_944382985.1_BRZ_EH_bin149_genomic.fna/dqc_result.json
[2023-06-28 02:22:42,692] [INFO] DFAST_QC completed!
[2023-06-28 02:22:42,692] [INFO] Total running time: 0h0m53s