[2023-06-29 15:18:14,379] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:18:14,381] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:18:14,381] [INFO] DQC Reference Directory: /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference
[2023-06-29 15:18:15,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:18:15,595] [INFO] Task started: Prodigal
[2023-06-29 15:18:15,595] [INFO] Running command: gunzip -c /var/lib/cwl/stg37d46cdc-da9a-48c6-b141-ed534f3154f3/GCA_910586595.1_MGBC152050_genomic.fna.gz | prodigal -d GCA_910586595.1_MGBC152050_genomic.fna/cds.fna -a GCA_910586595.1_MGBC152050_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:18:30,400] [INFO] Task succeeded: Prodigal
[2023-06-29 15:18:30,401] [INFO] Task started: HMMsearch
[2023-06-29 15:18:30,401] [INFO] Running command: hmmsearch --tblout GCA_910586595.1_MGBC152050_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/reference_markers.hmm GCA_910586595.1_MGBC152050_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:18:30,653] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:18:30,655] [INFO] Found 6/6 markers.
[2023-06-29 15:18:30,683] [INFO] Query marker FASTA was written to GCA_910586595.1_MGBC152050_genomic.fna/markers.fasta
[2023-06-29 15:18:30,683] [INFO] Task started: Blastn
[2023-06-29 15:18:30,683] [INFO] Running command: blastn -query GCA_910586595.1_MGBC152050_genomic.fna/markers.fasta -db /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/reference_markers.fasta -out GCA_910586595.1_MGBC152050_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:18:31,283] [INFO] Task succeeded: Blastn
[2023-06-29 15:18:31,287] [INFO] Selected 28 target genomes.
[2023-06-29 15:18:31,288] [INFO] Target genome list was writen to GCA_910586595.1_MGBC152050_genomic.fna/target_genomes.txt
[2023-06-29 15:18:31,288] [INFO] Task started: fastANI
[2023-06-29 15:18:31,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d46cdc-da9a-48c6-b141-ed534f3154f3/GCA_910586595.1_MGBC152050_genomic.fna.gz --refList GCA_910586595.1_MGBC152050_genomic.fna/target_genomes.txt --output GCA_910586595.1_MGBC152050_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:18:46,827] [INFO] Task succeeded: fastANI
[2023-06-29 15:18:46,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:18:46,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:18:46,841] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:18:46,842] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 15:18:46,842] [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
Duncaniella muris	strain=DSM 103720	GCA_003024805.1	2094150	2094150	type	True	77.1601	82	894	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.6871	73	894	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_002201515.1	1796646	1796646	type	True	76.6584	65	894	95	below_threshold
Duncaniella dubosii	strain=H5	GCA_004803915.1	2518971	2518971	type	True	76.6513	62	894	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_016696845.1	1796646	1796646	type	True	76.5975	67	894	95	below_threshold
Muribaculum intestinale	strain=YL27	GCA_001688845.2	1796646	1796646	type	True	76.5666	66	894	95	below_threshold
Heminiphilus faecis	strain=AM35	GCA_008728965.1	2601703	2601703	type	True	76.2514	59	894	95	below_threshold
Paramuribaculum intestinale	strain=DSM 100749	GCA_003024925.1	2094151	2094151	type	True	76.114	68	894	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 15:18:46,844] [INFO] DFAST Taxonomy check result was written to GCA_910586595.1_MGBC152050_genomic.fna/tc_result.tsv
[2023-06-29 15:18:46,845] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:18:46,845] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:18:46,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/checkm_data
[2023-06-29 15:18:46,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:18:46,876] [INFO] Task started: CheckM
[2023-06-29 15:18:46,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_910586595.1_MGBC152050_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_910586595.1_MGBC152050_genomic.fna/checkm_input GCA_910586595.1_MGBC152050_genomic.fna/checkm_result
[2023-06-29 15:19:32,227] [INFO] Task succeeded: CheckM
[2023-06-29 15:19:32,229] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:19:32,250] [INFO] ===== Completeness check finished =====
[2023-06-29 15:19:32,251] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:19:32,251] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_910586595.1_MGBC152050_genomic.fna/markers.fasta)
[2023-06-29 15:19:32,251] [INFO] Task started: Blastn
[2023-06-29 15:19:32,252] [INFO] Running command: blastn -query GCA_910586595.1_MGBC152050_genomic.fna/markers.fasta -db /var/lib/cwl/stg1683d805-1c73-409a-b51b-b716d37b52e2/dqc_reference/reference_markers_gtdb.fasta -out GCA_910586595.1_MGBC152050_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:19:33,087] [INFO] Task succeeded: Blastn
[2023-06-29 15:19:33,092] [INFO] Selected 19 target genomes.
[2023-06-29 15:19:33,092] [INFO] Target genome list was writen to GCA_910586595.1_MGBC152050_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:19:33,098] [INFO] Task started: fastANI
[2023-06-29 15:19:33,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg37d46cdc-da9a-48c6-b141-ed534f3154f3/GCA_910586595.1_MGBC152050_genomic.fna.gz --refList GCA_910586595.1_MGBC152050_genomic.fna/target_genomes_gtdb.txt --output GCA_910586595.1_MGBC152050_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:19:42,475] [INFO] Task succeeded: fastANI
[2023-06-29 15:19:42,495] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:19:42,495] [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_910586595.1	s__CAG-873 sp910586595	100.0	890	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014800815.1	s__CAG-873 sp014800815	78.304	202	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002493945.1	s__CAG-873 sp002493945	78.1744	244	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.61	97.51	0.95	0.88	8	-
GCA_009775225.1	s__CAG-873 sp009775225	77.9895	205	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.13	98.13	0.88	0.86	3	-
GCA_910587355.1	s__CAG-873 sp910587355	77.9576	181	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548975.1	s__CAG-873 sp900548975	77.8584	171	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.98	99.96	0.94	0.89	3	-
GCA_910579995.1	s__CAG-873 sp009775135	77.8385	188	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.86	99.86	0.96	0.96	2	-
GCA_910578035.1	s__CAG-873 sp910578035	77.8045	152	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003979155.1	s__CAG-873 sp003979155	77.6943	124	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	99.69	99.57	0.90	0.86	3	-
GCA_014800735.1	s__CAG-873 sp014800735	77.5619	158	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.24	97.04	0.84	0.82	3	-
GCA_009775195.1	s__CAG-873 sp009775195	77.5394	152	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.01	95.47	0.84	0.74	3	-
GCA_905202215.1	s__CAG-873 sp905202215	77.4969	159	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.54	98.54	0.91	0.91	2	-
GCA_910579035.1	s__CAG-873 sp011959565	77.485	159	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.99	96.96	0.89	0.75	5	-
GCA_910583525.1	s__CAG-873 sp910583525	77.4776	192	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555715.1	s__CAG-873 sp900555715	77.1643	133	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	97.36	96.57	0.81	0.79	3	-
GCA_014802445.1	s__CAG-1031 sp014802445	77.1469	82	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-1031	95.0	98.18	98.18	0.94	0.94	2	-
GCA_009775125.1	s__CAG-873 sp001689665	76.8675	103	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.51	97.14	0.87	0.85	3	-
GCA_014801075.1	s__UBA7173 sp014801075	76.7737	92	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__UBA7173	95.0	97.74	97.55	0.90	0.88	4	-
GCA_004553485.1	s__CAG-873 sp004553485	76.6069	95	894	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__CAG-873	95.0	98.24	98.24	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-29 15:19:42,498] [INFO] GTDB search result was written to GCA_910586595.1_MGBC152050_genomic.fna/result_gtdb.tsv
[2023-06-29 15:19:42,498] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:19:42,502] [INFO] DFAST_QC result json was written to GCA_910586595.1_MGBC152050_genomic.fna/dqc_result.json
[2023-06-29 15:19:42,502] [INFO] DFAST_QC completed!
[2023-06-29 15:19:42,502] [INFO] Total running time: 0h1m28s