[2024-01-24 12:53:49,413] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:49,416] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:49,416] [INFO] DQC Reference Directory: /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference
[2024-01-24 12:53:51,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:51,732] [INFO] Task started: Prodigal
[2024-01-24 12:53:51,732] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c46cb17-5c84-4bc6-9d2d-3f4675e87841/GCF_000621725.1_ASM62172v1_genomic.fna.gz | prodigal -d GCF_000621725.1_ASM62172v1_genomic.fna/cds.fna -a GCF_000621725.1_ASM62172v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:11,460] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:11,460] [INFO] Task started: HMMsearch
[2024-01-24 12:54:11,460] [INFO] Running command: hmmsearch --tblout GCF_000621725.1_ASM62172v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/reference_markers.hmm GCF_000621725.1_ASM62172v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:11,725] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:11,726] [INFO] Found 6/6 markers.
[2024-01-24 12:54:11,758] [INFO] Query marker FASTA was written to GCF_000621725.1_ASM62172v1_genomic.fna/markers.fasta
[2024-01-24 12:54:11,758] [INFO] Task started: Blastn
[2024-01-24 12:54:11,758] [INFO] Running command: blastn -query GCF_000621725.1_ASM62172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/reference_markers.fasta -out GCF_000621725.1_ASM62172v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:12,347] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:12,351] [INFO] Selected 20 target genomes.
[2024-01-24 12:54:12,352] [INFO] Target genome list was writen to GCF_000621725.1_ASM62172v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:12,422] [INFO] Task started: fastANI
[2024-01-24 12:54:12,422] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c46cb17-5c84-4bc6-9d2d-3f4675e87841/GCF_000621725.1_ASM62172v1_genomic.fna.gz --refList GCF_000621725.1_ASM62172v1_genomic.fna/target_genomes.txt --output GCF_000621725.1_ASM62172v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:54:23,399] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:23,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:54:23,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:54:23,414] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:54:23,415] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:54:23,415] [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
Prevotella brevis	strain=ATCC 19188	GCA_000621725.1	83231	83231	type	True	100.0	1144	1148	95	conclusive
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	79.2102	251	1148	95	below_threshold
Prevotella ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	79.1688	255	1148	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.1012	99	1148	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.2339	104	1148	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.1958	102	1148	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	77.0772	106	1148	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.924	73	1148	95	below_threshold
Prevotella dentasini	strain=JCM 15908	GCA_000614065.1	589537	589537	type	True	76.6957	53	1148	95	below_threshold
Xylanibacter muris	strain=PMUR	GCA_013166605.1	2736290	2736290	type	True	76.6832	50	1148	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.1485	59	1148	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:54:23,418] [INFO] DFAST Taxonomy check result was written to GCF_000621725.1_ASM62172v1_genomic.fna/tc_result.tsv
[2024-01-24 12:54:23,420] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:54:23,420] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:54:23,421] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/checkm_data
[2024-01-24 12:54:23,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:54:23,463] [INFO] Task started: CheckM
[2024-01-24 12:54:23,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000621725.1_ASM62172v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000621725.1_ASM62172v1_genomic.fna/checkm_input GCF_000621725.1_ASM62172v1_genomic.fna/checkm_result
[2024-01-24 12:55:23,141] [INFO] Task succeeded: CheckM
[2024-01-24 12:55:23,143] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:55:23,163] [INFO] ===== Completeness check finished =====
[2024-01-24 12:55:23,164] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:55:23,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000621725.1_ASM62172v1_genomic.fna/markers.fasta)
[2024-01-24 12:55:23,165] [INFO] Task started: Blastn
[2024-01-24 12:55:23,165] [INFO] Running command: blastn -query GCF_000621725.1_ASM62172v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77871d71-cb03-4eb7-b63a-0145d5b03e8c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000621725.1_ASM62172v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:55:24,094] [INFO] Task succeeded: Blastn
[2024-01-24 12:55:24,099] [INFO] Selected 22 target genomes.
[2024-01-24 12:55:24,099] [INFO] Target genome list was writen to GCF_000621725.1_ASM62172v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:55:24,193] [INFO] Task started: fastANI
[2024-01-24 12:55:24,193] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c46cb17-5c84-4bc6-9d2d-3f4675e87841/GCF_000621725.1_ASM62172v1_genomic.fna.gz --refList GCF_000621725.1_ASM62172v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000621725.1_ASM62172v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:55:37,198] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:37,218] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:55:37,219] [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
GCF_000621725.1	s__Prevotella brevis	100.0	1144	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.58	97.58	0.89	0.89	2	conclusive
GCF_900100635.1	s__Prevotella sp900100635	80.0711	362	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.15	96.60	0.86	0.83	10	-
GCA_900119285.1	s__Prevotella sp900119285	79.571	197	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.20	98.20	0.84	0.84	2	-
GCA_902778255.1	s__Prevotella sp902778255	79.4157	324	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.79	98.79	0.87	0.87	2	-
GCA_902785695.1	s__Prevotella sp902785695	79.3929	227	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799975.1	s__Prevotella sp902799975	79.2468	280	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775605.1	s__Prevotella sp902775605	79.1973	295	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799355.1	s__Prevotella sp902799355	79.0805	218	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.80	96.48	0.80	0.78	3	-
GCA_900313235.1	s__Prevotella sp900313235	78.733	222	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017483805.1	s__Prevotella sp017483805	78.7297	302	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799905.1	s__Prevotella sp902799905	78.6135	296	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.33	98.29	0.89	0.87	3	-
GCF_900107705.1	s__Prevotella sp900107705	78.5841	201	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.93	97.93	0.92	0.92	2	-
GCA_017458225.1	s__Prevotella sp017458225	78.5697	225	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902798425.1	s__Prevotella sp902798425	78.468	237	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.06	97.06	0.85	0.85	2	-
GCA_017455845.1	s__Prevotella sp017455845	78.3517	227	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775475.1	s__Prevotella sp902775475	78.2365	275	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.69	98.51	0.89	0.87	7	-
GCA_017941345.1	s__Prevotella sp017941345	78.132	125	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320445.1	s__Prevotella sp900320445	78.0957	227	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.78	96.58	0.88	0.79	4	-
GCA_017447515.1	s__Prevotella sp017447515	78.0838	122	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779455.1	s__Prevotella sp902779455	77.7431	254	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470345.1	s__Prevotella sp017470345	77.7031	179	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002361655.1	s__Prevotella sp002361655	77.6381	223	1148	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:55:37,220] [INFO] GTDB search result was written to GCF_000621725.1_ASM62172v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:55:37,221] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:55:37,225] [INFO] DFAST_QC result json was written to GCF_000621725.1_ASM62172v1_genomic.fna/dqc_result.json
[2024-01-24 12:55:37,226] [INFO] DFAST_QC completed!
[2024-01-24 12:55:37,226] [INFO] Total running time: 0h1m48s