[2023-06-13 03:40:46,616] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:40:46,619] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:40:46,620] [INFO] DQC Reference Directory: /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference
[2023-06-13 03:40:48,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:40:48,942] [INFO] Task started: Prodigal
[2023-06-13 03:40:48,942] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bafe75f-ccc1-4542-a658-a3de967a59c6/GCA_022787565.1_ASM2278756v1_genomic.fna.gz | prodigal -d GCA_022787565.1_ASM2278756v1_genomic.fna/cds.fna -a GCA_022787565.1_ASM2278756v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:40:56,093] [INFO] Task succeeded: Prodigal
[2023-06-13 03:40:56,094] [INFO] Task started: HMMsearch
[2023-06-13 03:40:56,094] [INFO] Running command: hmmsearch --tblout GCA_022787565.1_ASM2278756v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/reference_markers.hmm GCA_022787565.1_ASM2278756v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:40:56,324] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:40:56,325] [INFO] Found 6/6 markers.
[2023-06-13 03:40:56,353] [INFO] Query marker FASTA was written to GCA_022787565.1_ASM2278756v1_genomic.fna/markers.fasta
[2023-06-13 03:40:56,354] [INFO] Task started: Blastn
[2023-06-13 03:40:56,354] [INFO] Running command: blastn -query GCA_022787565.1_ASM2278756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/reference_markers.fasta -out GCA_022787565.1_ASM2278756v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:40:56,954] [INFO] Task succeeded: Blastn
[2023-06-13 03:40:56,959] [INFO] Selected 19 target genomes.
[2023-06-13 03:40:56,960] [INFO] Target genome list was writen to GCA_022787565.1_ASM2278756v1_genomic.fna/target_genomes.txt
[2023-06-13 03:40:56,964] [INFO] Task started: fastANI
[2023-06-13 03:40:56,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bafe75f-ccc1-4542-a658-a3de967a59c6/GCA_022787565.1_ASM2278756v1_genomic.fna.gz --refList GCA_022787565.1_ASM2278756v1_genomic.fna/target_genomes.txt --output GCA_022787565.1_ASM2278756v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:41:05,319] [INFO] Task succeeded: fastANI
[2023-06-13 03:41:05,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:41:05,320] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:41:05,337] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:41:05,337] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 03:41:05,337] [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
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	77.936	113	843	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.6189	94	843	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.461	110	843	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	77.3848	129	843	95	below_threshold
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.2913	89	843	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	77.1403	121	843	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	77.1204	117	843	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	77.0937	69	843	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	76.8457	77	843	95	below_threshold
Bittarella massiliensis	strain=GD6	GCA_001486165.1	1720313	1720313	type	True	76.7977	63	843	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_003425665.1	2211183	2211183	type	True	76.7787	58	843	95	below_threshold
Evtepia gabavorous	strain=KLE1738	GCA_008121455.1	2211183	2211183	type	True	76.7787	58	843	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 03:41:05,489] [INFO] DFAST Taxonomy check result was written to GCA_022787565.1_ASM2278756v1_genomic.fna/tc_result.tsv
[2023-06-13 03:41:05,489] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:41:05,490] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:41:05,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/checkm_data
[2023-06-13 03:41:05,492] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:41:05,521] [INFO] Task started: CheckM
[2023-06-13 03:41:05,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022787565.1_ASM2278756v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022787565.1_ASM2278756v1_genomic.fna/checkm_input GCA_022787565.1_ASM2278756v1_genomic.fna/checkm_result
[2023-06-13 03:41:32,271] [INFO] Task succeeded: CheckM
[2023-06-13 03:41:32,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:41:32,299] [INFO] ===== Completeness check finished =====
[2023-06-13 03:41:32,300] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:41:32,300] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022787565.1_ASM2278756v1_genomic.fna/markers.fasta)
[2023-06-13 03:41:32,301] [INFO] Task started: Blastn
[2023-06-13 03:41:32,301] [INFO] Running command: blastn -query GCA_022787565.1_ASM2278756v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga32f3c17-246a-47de-87b6-5d9115abbb1e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022787565.1_ASM2278756v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:41:33,239] [INFO] Task succeeded: Blastn
[2023-06-13 03:41:33,243] [INFO] Selected 24 target genomes.
[2023-06-13 03:41:33,243] [INFO] Target genome list was writen to GCA_022787565.1_ASM2278756v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:41:33,273] [INFO] Task started: fastANI
[2023-06-13 03:41:33,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bafe75f-ccc1-4542-a658-a3de967a59c6/GCA_022787565.1_ASM2278756v1_genomic.fna.gz --refList GCA_022787565.1_ASM2278756v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022787565.1_ASM2278756v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:41:43,718] [INFO] Task succeeded: fastANI
[2023-06-13 03:41:43,746] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 03:41:43,746] [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_004560305.1	s__Limivicinus sp004560305	81.3081	256	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	96.68	96.68	0.69	0.69	2	-
GCA_900319635.1	s__Limivicinus sp900319635	80.4855	250	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.84	96.83	0.85	0.76	6	-
GCA_017470325.1	s__Limivicinus sp017470325	80.4	231	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316205.1	s__Limivicinus sp900316205	80.0103	257	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.11	98.31	0.88	0.81	3	-
GCA_900319835.1	s__Limivicinus sp900319835	79.9862	226	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_902778275.1	s__Limivicinus sp902778275	79.9689	263	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018711755.1	s__Limivicinus faecipullorum	79.9509	228	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545165.1	s__Limivicinus sp017545165	79.9127	210	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765595.1	s__Limivicinus sp002350825	79.8837	253	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.80	99.80	0.90	0.90	2	-
GCA_902775985.1	s__Limivicinus sp902775985	79.8559	246	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.70	98.45	0.76	0.73	5	-
GCA_902787755.1	s__Limivicinus sp902787755	79.8157	243	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316255.1	s__Limivicinus sp900316255	79.7517	258	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.92	95.41	0.88	0.79	4	-
GCA_017428565.1	s__Limivicinus sp017428565	79.7197	269	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775355.1	s__Limivicinus sp902775355	79.531	263	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320035.1	s__Limivicinus sp002320035	79.4351	222	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.95	98.71	0.80	0.75	5	-
GCA_902778285.1	s__Limivicinus sp902778285	79.2233	240	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.33	98.33	0.79	0.79	2	-
GCA_902795045.1	s__Limivicinus sp902795045	79.0354	230	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.71	97.45	0.84	0.77	4	-
GCA_017477695.1	s__Limivicinus sp017477695	79.0307	187	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790375.1	s__Limivicinus sp902790375	79.0123	216	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900754515.1	s__Limivicinus sp900754515	78.9326	212	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	97.83	97.83	0.85	0.85	2	-
GCA_900549645.1	s__Limivicinus sp900549645	78.9066	207	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	-
GCA_902761635.1	s__Limivicinus sp902761635	78.7386	215	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547315.1	s__Limivicinus sp900547315	78.7045	205	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_017430985.1	s__Limivicinus sp017430985	78.5716	202	843	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 03:41:43,748] [INFO] GTDB search result was written to GCA_022787565.1_ASM2278756v1_genomic.fna/result_gtdb.tsv
[2023-06-13 03:41:43,749] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:41:43,753] [INFO] DFAST_QC result json was written to GCA_022787565.1_ASM2278756v1_genomic.fna/dqc_result.json
[2023-06-13 03:41:43,753] [INFO] DFAST_QC completed!
[2023-06-13 03:41:43,754] [INFO] Total running time: 0h0m57s