[2023-07-01 01:38:06,107] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:38:06,110] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:38:06,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference
[2023-07-01 01:38:07,447] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:38:07,448] [INFO] Task started: Prodigal
[2023-07-01 01:38:07,448] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dc488f9-c40e-403b-b742-1b0b01154dc7/GCA_900768175.1_SRS476092_45_genomic.fna.gz | prodigal -d GCA_900768175.1_SRS476092_45_genomic.fna/cds.fna -a GCA_900768175.1_SRS476092_45_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:38:26,552] [INFO] Task succeeded: Prodigal
[2023-07-01 01:38:26,553] [INFO] Task started: HMMsearch
[2023-07-01 01:38:26,553] [INFO] Running command: hmmsearch --tblout GCA_900768175.1_SRS476092_45_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/reference_markers.hmm GCA_900768175.1_SRS476092_45_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:38:26,773] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:38:26,775] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7dc488f9-c40e-403b-b742-1b0b01154dc7/GCA_900768175.1_SRS476092_45_genomic.fna.gz]
[2023-07-01 01:38:26,811] [INFO] Query marker FASTA was written to GCA_900768175.1_SRS476092_45_genomic.fna/markers.fasta
[2023-07-01 01:38:26,812] [INFO] Task started: Blastn
[2023-07-01 01:38:26,812] [INFO] Running command: blastn -query GCA_900768175.1_SRS476092_45_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/reference_markers.fasta -out GCA_900768175.1_SRS476092_45_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:38:27,357] [INFO] Task succeeded: Blastn
[2023-07-01 01:38:27,362] [INFO] Selected 14 target genomes.
[2023-07-01 01:38:27,363] [INFO] Target genome list was writen to GCA_900768175.1_SRS476092_45_genomic.fna/target_genomes.txt
[2023-07-01 01:38:27,364] [INFO] Task started: fastANI
[2023-07-01 01:38:27,365] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc488f9-c40e-403b-b742-1b0b01154dc7/GCA_900768175.1_SRS476092_45_genomic.fna.gz --refList GCA_900768175.1_SRS476092_45_genomic.fna/target_genomes.txt --output GCA_900768175.1_SRS476092_45_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:38:34,791] [INFO] Task succeeded: fastANI
[2023-07-01 01:38:34,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:38:34,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:38:34,810] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:38:34,810] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:38:34,810] [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 copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	84.3583	353	1025	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	84.1949	372	1025	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	84.1644	363	1025	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	82.5378	339	1025	95	below_threshold
Hallella faecis	strain=CLA-AA-H145	GCA_018789675.1	2841596	2841596	type	True	78.1894	73	1025	95	below_threshold
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	78.1257	88	1025	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	78.0843	58	1025	95	below_threshold
Prevotella fusca	strain=W1435	GCA_001262015.1	589436	589436	type	True	77.6459	57	1025	95	below_threshold
Prevotella albensis	strain=DSM 11370	GCA_000426565.1	77768	77768	type	True	77.4779	76	1025	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.3498	77	1025	95	below_threshold
Prevotella paludivivens	strain=DSM 17968	GCA_000373185.1	185294	185294	type	True	77.1412	52	1025	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:38:34,813] [INFO] DFAST Taxonomy check result was written to GCA_900768175.1_SRS476092_45_genomic.fna/tc_result.tsv
[2023-07-01 01:38:34,813] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:38:34,814] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:38:34,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/checkm_data
[2023-07-01 01:38:34,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:38:34,860] [INFO] Task started: CheckM
[2023-07-01 01:38:34,860] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_900768175.1_SRS476092_45_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_900768175.1_SRS476092_45_genomic.fna/checkm_input GCA_900768175.1_SRS476092_45_genomic.fna/checkm_result
[2023-07-01 01:39:30,727] [INFO] Task succeeded: CheckM
[2023-07-01 01:39:30,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:39:30,751] [INFO] ===== Completeness check finished =====
[2023-07-01 01:39:30,751] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:39:30,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_900768175.1_SRS476092_45_genomic.fna/markers.fasta)
[2023-07-01 01:39:30,752] [INFO] Task started: Blastn
[2023-07-01 01:39:30,752] [INFO] Running command: blastn -query GCA_900768175.1_SRS476092_45_genomic.fna/markers.fasta -db /var/lib/cwl/stg62a6bd7e-2c56-4d57-ad83-23e9397cab79/dqc_reference/reference_markers_gtdb.fasta -out GCA_900768175.1_SRS476092_45_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:39:31,251] [INFO] Task succeeded: Blastn
[2023-07-01 01:39:31,256] [INFO] Selected 16 target genomes.
[2023-07-01 01:39:31,256] [INFO] Target genome list was writen to GCA_900768175.1_SRS476092_45_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:39:31,261] [INFO] Task started: fastANI
[2023-07-01 01:39:31,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dc488f9-c40e-403b-b742-1b0b01154dc7/GCA_900768175.1_SRS476092_45_genomic.fna.gz --refList GCA_900768175.1_SRS476092_45_genomic.fna/target_genomes_gtdb.txt --output GCA_900768175.1_SRS476092_45_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:39:40,429] [INFO] Task succeeded: fastANI
[2023-07-01 01:39:40,450] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 01:39:40,451] [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_000436035.1	s__Prevotella sp000436035	92.9082	399	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.58	97.92	0.86	0.81	4	-
GCA_019249655.1	s__Prevotella sp900767615	86.8996	429	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_019127135.1	s__Prevotella sp900551275	86.4041	419	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900555035.1	s__Prevotella sp900555035	85.1484	323	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015074785.1	s__Prevotella sp015074785	84.7408	407	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCA_900557255.1	s__Prevotella sp900557255	84.4618	273	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000157935.1	s__Prevotella copri	84.2356	370	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900551985.1	s__Prevotella sp900551985	83.1796	318	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCF_004535825.1	s__Prevotella hominis	82.5381	339	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.52	95.16	0.76	0.66	13	-
GCA_900765465.1	s__Prevotella sp900765465	82.4714	183	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548535.1	s__Prevotella sp900548535	82.4483	290	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554835.1	s__Prevotella sp900554835	82.1889	294	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002297965.1	s__Prevotella sp002297965	81.4074	248	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.14	99.14	0.78	0.78	2	-
GCA_002440225.1	s__Prevotella sp002440225	81.3311	275	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.88	98.88	0.81	0.81	2	-
GCA_002451555.1	s__Prevotella sp002451555	81.0774	270	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.47	99.47	0.85	0.85	2	-
GCA_002405875.1	s__Prevotella sp002405875	80.2933	137	1025	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:39:40,453] [INFO] GTDB search result was written to GCA_900768175.1_SRS476092_45_genomic.fna/result_gtdb.tsv
[2023-07-01 01:39:40,453] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:39:40,457] [INFO] DFAST_QC result json was written to GCA_900768175.1_SRS476092_45_genomic.fna/dqc_result.json
[2023-07-01 01:39:40,457] [INFO] DFAST_QC completed!
[2023-07-01 01:39:40,457] [INFO] Total running time: 0h1m34s