[2023-06-29 14:09:56,542] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:09:56,544] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:09:56,544] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference
[2023-06-29 14:09:57,761] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:09:57,762] [INFO] Task started: Prodigal
[2023-06-29 14:09:57,762] [INFO] Running command: gunzip -c /var/lib/cwl/stgbcf7d654-2235-432c-a647-a1cca1142fce/GCA_023708205.1_ASM2370820v1_genomic.fna.gz | prodigal -d GCA_023708205.1_ASM2370820v1_genomic.fna/cds.fna -a GCA_023708205.1_ASM2370820v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:10:11,284] [INFO] Task succeeded: Prodigal
[2023-06-29 14:10:11,285] [INFO] Task started: HMMsearch
[2023-06-29 14:10:11,285] [INFO] Running command: hmmsearch --tblout GCA_023708205.1_ASM2370820v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/reference_markers.hmm GCA_023708205.1_ASM2370820v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:10:11,516] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:10:11,517] [INFO] Found 6/6 markers.
[2023-06-29 14:10:11,546] [INFO] Query marker FASTA was written to GCA_023708205.1_ASM2370820v1_genomic.fna/markers.fasta
[2023-06-29 14:10:11,546] [INFO] Task started: Blastn
[2023-06-29 14:10:11,546] [INFO] Running command: blastn -query GCA_023708205.1_ASM2370820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/reference_markers.fasta -out GCA_023708205.1_ASM2370820v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:10:12,164] [INFO] Task succeeded: Blastn
[2023-06-29 14:10:12,169] [INFO] Selected 25 target genomes.
[2023-06-29 14:10:12,170] [INFO] Target genome list was writen to GCA_023708205.1_ASM2370820v1_genomic.fna/target_genomes.txt
[2023-06-29 14:10:12,172] [INFO] Task started: fastANI
[2023-06-29 14:10:12,172] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf7d654-2235-432c-a647-a1cca1142fce/GCA_023708205.1_ASM2370820v1_genomic.fna.gz --refList GCA_023708205.1_ASM2370820v1_genomic.fna/target_genomes.txt --output GCA_023708205.1_ASM2370820v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:10:29,046] [INFO] Task succeeded: fastANI
[2023-06-29 14:10:29,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:10:29,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:10:29,062] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:10:29,062] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:10:29,062] [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
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.6119	79	791	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.579	96	791	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	77.5235	95	791	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	77.5211	95	791	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.1555	107	791	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.0504	116	791	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	76.9579	91	791	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.7703	107	791	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.5219	68	791	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	76.4891	67	791	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.3362	82	791	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.3287	69	791	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	76.2539	71	791	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:10:29,064] [INFO] DFAST Taxonomy check result was written to GCA_023708205.1_ASM2370820v1_genomic.fna/tc_result.tsv
[2023-06-29 14:10:29,065] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:10:29,065] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:10:29,065] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/checkm_data
[2023-06-29 14:10:29,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:10:29,091] [INFO] Task started: CheckM
[2023-06-29 14:10:29,091] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708205.1_ASM2370820v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708205.1_ASM2370820v1_genomic.fna/checkm_input GCA_023708205.1_ASM2370820v1_genomic.fna/checkm_result
[2023-06-29 14:11:08,772] [INFO] Task succeeded: CheckM
[2023-06-29 14:11:08,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 14:11:08,794] [INFO] ===== Completeness check finished =====
[2023-06-29 14:11:08,795] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:11:08,795] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708205.1_ASM2370820v1_genomic.fna/markers.fasta)
[2023-06-29 14:11:08,796] [INFO] Task started: Blastn
[2023-06-29 14:11:08,796] [INFO] Running command: blastn -query GCA_023708205.1_ASM2370820v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cb2aab7-fecf-4ac7-8567-0bb3472ca21d/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708205.1_ASM2370820v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:11:09,653] [INFO] Task succeeded: Blastn
[2023-06-29 14:11:09,658] [INFO] Selected 14 target genomes.
[2023-06-29 14:11:09,658] [INFO] Target genome list was writen to GCA_023708205.1_ASM2370820v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:11:09,662] [INFO] Task started: fastANI
[2023-06-29 14:11:09,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgbcf7d654-2235-432c-a647-a1cca1142fce/GCA_023708205.1_ASM2370820v1_genomic.fna.gz --refList GCA_023708205.1_ASM2370820v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708205.1_ASM2370820v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:11:15,338] [INFO] Task succeeded: fastANI
[2023-06-29 14:11:15,351] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:11:15,351] [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_900104605.1	s__Tidjanibacter inops_A	98.9261	729	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	99.31	98.92	0.96	0.89	16	conclusive
GCA_019114205.1	s__Tidjanibacter gallistercoris	83.1123	499	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577285.1	s__Tidjanibacter sp910577285	82.7743	508	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	79.2865	273	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000154465.1	s__Alistipes putredinis	77.6638	77	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.94	97.62	0.91	0.76	28	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.4719	84	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_017935625.1	s__RGIG9113 sp017935625	77.1538	108	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014982715.1	s__DSM-108975 sp014982715	77.0751	114	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	76.9997	93	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900546065.1	s__Alistipes merdipullorum	76.2819	60	791	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.89	97.88	0.91	0.90	3	-
--------------------------------------------------------------------------------
[2023-06-29 14:11:15,353] [INFO] GTDB search result was written to GCA_023708205.1_ASM2370820v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:11:15,354] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:11:15,357] [INFO] DFAST_QC result json was written to GCA_023708205.1_ASM2370820v1_genomic.fna/dqc_result.json
[2023-06-29 14:11:15,358] [INFO] DFAST_QC completed!
[2023-06-29 14:11:15,358] [INFO] Total running time: 0h1m19s