[2023-06-29 12:41:09,832] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:41:09,835] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:41:09,835] [INFO] DQC Reference Directory: /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference
[2023-06-29 12:41:11,150] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:41:11,150] [INFO] Task started: Prodigal
[2023-06-29 12:41:11,151] [INFO] Running command: gunzip -c /var/lib/cwl/stgd8c84b6f-7050-4baf-9f20-28dba2f6626a/GCA_023708305.1_ASM2370830v1_genomic.fna.gz | prodigal -d GCA_023708305.1_ASM2370830v1_genomic.fna/cds.fna -a GCA_023708305.1_ASM2370830v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:24,951] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:24,951] [INFO] Task started: HMMsearch
[2023-06-29 12:41:24,951] [INFO] Running command: hmmsearch --tblout GCA_023708305.1_ASM2370830v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/reference_markers.hmm GCA_023708305.1_ASM2370830v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:25,210] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:25,212] [INFO] Found 6/6 markers.
[2023-06-29 12:41:25,235] [INFO] Query marker FASTA was written to GCA_023708305.1_ASM2370830v1_genomic.fna/markers.fasta
[2023-06-29 12:41:25,236] [INFO] Task started: Blastn
[2023-06-29 12:41:25,236] [INFO] Running command: blastn -query GCA_023708305.1_ASM2370830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/reference_markers.fasta -out GCA_023708305.1_ASM2370830v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:25,838] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:25,843] [INFO] Selected 25 target genomes.
[2023-06-29 12:41:25,844] [INFO] Target genome list was writen to GCA_023708305.1_ASM2370830v1_genomic.fna/target_genomes.txt
[2023-06-29 12:41:25,852] [INFO] Task started: fastANI
[2023-06-29 12:41:25,852] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8c84b6f-7050-4baf-9f20-28dba2f6626a/GCA_023708305.1_ASM2370830v1_genomic.fna.gz --refList GCA_023708305.1_ASM2370830v1_genomic.fna/target_genomes.txt --output GCA_023708305.1_ASM2370830v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:43,813] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:43,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:43,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:43,830] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:41:43,830] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:41:43,831] [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 shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	77.6182	96	799	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	77.4927	96	799	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	77.4711	110	799	95	below_threshold
Alistipes putredinis	strain=DSM 17216	GCA_000154465.1	28117	28117	type	True	77.4527	77	799	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.41	94	799	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	77.1872	111	799	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	77.1074	96	799	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	77.0875	69	799	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.0849	69	799	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.9978	109	799	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	76.8695	67	799	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.7421	85	799	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	76.5612	66	799	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:41:43,833] [INFO] DFAST Taxonomy check result was written to GCA_023708305.1_ASM2370830v1_genomic.fna/tc_result.tsv
[2023-06-29 12:41:43,833] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:43,833] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:43,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/checkm_data
[2023-06-29 12:41:43,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:43,864] [INFO] Task started: CheckM
[2023-06-29 12:41:43,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708305.1_ASM2370830v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708305.1_ASM2370830v1_genomic.fna/checkm_input GCA_023708305.1_ASM2370830v1_genomic.fna/checkm_result
[2023-06-29 12:42:24,979] [INFO] Task succeeded: CheckM
[2023-06-29 12:42:24,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:42:25,000] [INFO] ===== Completeness check finished =====
[2023-06-29 12:42:25,000] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:42:25,001] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708305.1_ASM2370830v1_genomic.fna/markers.fasta)
[2023-06-29 12:42:25,002] [INFO] Task started: Blastn
[2023-06-29 12:42:25,002] [INFO] Running command: blastn -query GCA_023708305.1_ASM2370830v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8b88c9f2-46e4-4f97-8a70-224c66a41ee9/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708305.1_ASM2370830v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:42:26,151] [INFO] Task succeeded: Blastn
[2023-06-29 12:42:26,156] [INFO] Selected 14 target genomes.
[2023-06-29 12:42:26,157] [INFO] Target genome list was writen to GCA_023708305.1_ASM2370830v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:42:26,169] [INFO] Task started: fastANI
[2023-06-29 12:42:26,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8c84b6f-7050-4baf-9f20-28dba2f6626a/GCA_023708305.1_ASM2370830v1_genomic.fna.gz --refList GCA_023708305.1_ASM2370830v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708305.1_ASM2370830v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:42:32,737] [INFO] Task succeeded: fastANI
[2023-06-29 12:42:32,752] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:42:32,752] [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	98.9366	732	799	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	83.1258	492	799	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	82.6697	495	799	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	79.1056	263	799	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	77.4924	76	799	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	77.4605	86	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_014982715.1	s__DSM-108975 sp014982715	77.1899	110	799	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_900546065.1	s__Alistipes merdipullorum	76.921	56	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.89	97.88	0.91	0.90	3	-
GCA_017935625.1	s__RGIG9113 sp017935625	76.8622	116	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910576555.1	s__Alistipes sp910576555	76.7754	98	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549685.1	s__Alistipes_A sp900549685	76.5208	55	799	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:42:32,754] [INFO] GTDB search result was written to GCA_023708305.1_ASM2370830v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:42:32,755] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:42:32,759] [INFO] DFAST_QC result json was written to GCA_023708305.1_ASM2370830v1_genomic.fna/dqc_result.json
[2023-06-29 12:42:32,759] [INFO] DFAST_QC completed!
[2023-06-29 12:42:32,759] [INFO] Total running time: 0h1m23s