[2024-01-24 12:36:58,575] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:58,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:58,578] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference
[2024-01-24 12:36:59,901] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:59,902] [INFO] Task started: Prodigal
[2024-01-24 12:36:59,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cccc424-5fdc-4528-98d7-180f509f1d1c/GCF_014288115.1_ASM1428811v1_genomic.fna.gz | prodigal -d GCF_014288115.1_ASM1428811v1_genomic.fna/cds.fna -a GCF_014288115.1_ASM1428811v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:15,214] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:15,214] [INFO] Task started: HMMsearch
[2024-01-24 12:37:15,214] [INFO] Running command: hmmsearch --tblout GCF_014288115.1_ASM1428811v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/reference_markers.hmm GCF_014288115.1_ASM1428811v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:15,537] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:15,538] [INFO] Found 6/6 markers.
[2024-01-24 12:37:15,564] [INFO] Query marker FASTA was written to GCF_014288115.1_ASM1428811v1_genomic.fna/markers.fasta
[2024-01-24 12:37:15,565] [INFO] Task started: Blastn
[2024-01-24 12:37:15,565] [INFO] Running command: blastn -query GCF_014288115.1_ASM1428811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/reference_markers.fasta -out GCF_014288115.1_ASM1428811v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:16,211] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:16,215] [INFO] Selected 14 target genomes.
[2024-01-24 12:37:16,216] [INFO] Target genome list was writen to GCF_014288115.1_ASM1428811v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:16,247] [INFO] Task started: fastANI
[2024-01-24 12:37:16,247] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cccc424-5fdc-4528-98d7-180f509f1d1c/GCF_014288115.1_ASM1428811v1_genomic.fna.gz --refList GCF_014288115.1_ASM1428811v1_genomic.fna/target_genomes.txt --output GCF_014288115.1_ASM1428811v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:23,397] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:23,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:23,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:23,409] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:37:23,410] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:37:23,410] [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
Rikenella microfusus	strain=NCTC11190	GCA_900455755.1	28139	28139	type	True	78.6878	119	954	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_025144665.1	1470347	1470347	type	True	78.682	345	954	95	below_threshold
Alistipes ihumii	strain=AP11	GCA_000321205.1	1470347	1470347	type	True	78.6727	340	954	95	below_threshold
Rikenella microfusus	strain=DSM 15922	GCA_000427365.1	28139	28139	type	True	78.6569	120	954	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	78.5749	125	954	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	78.5501	177	954	95	below_threshold
Alistipes onderdonkii	strain=DSM 19147	GCA_000374505.1	328813	328813	type	True	78.3626	128	954	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	78.0696	125	954	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	77.889	226	954	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	77.8626	226	954	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.5949	133	954	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	76.4816	123	954	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:23,412] [INFO] DFAST Taxonomy check result was written to GCF_014288115.1_ASM1428811v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:23,413] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:23,413] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:23,413] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/checkm_data
[2024-01-24 12:37:23,415] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:23,451] [INFO] Task started: CheckM
[2024-01-24 12:37:23,451] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014288115.1_ASM1428811v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014288115.1_ASM1428811v1_genomic.fna/checkm_input GCF_014288115.1_ASM1428811v1_genomic.fna/checkm_result
[2024-01-24 12:38:08,284] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:08,286] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:08,326] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:08,327] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:08,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014288115.1_ASM1428811v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:08,328] [INFO] Task started: Blastn
[2024-01-24 12:38:08,328] [INFO] Running command: blastn -query GCF_014288115.1_ASM1428811v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1da3b74-9241-469a-91d5-f417ae3e22f7/dqc_reference/reference_markers_gtdb.fasta -out GCF_014288115.1_ASM1428811v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:09,276] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:09,280] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:09,280] [INFO] Target genome list was writen to GCF_014288115.1_ASM1428811v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:09,301] [INFO] Task started: fastANI
[2024-01-24 12:38:09,301] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cccc424-5fdc-4528-98d7-180f509f1d1c/GCF_014288115.1_ASM1428811v1_genomic.fna.gz --refList GCF_014288115.1_ASM1428811v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014288115.1_ASM1428811v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:15,233] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:15,247] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:15,247] [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_009557455.1	s__Alistipes_A pullistercoris	99.3883	905	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.39	98.63	0.95	0.90	13	conclusive
GCA_910575495.1	s__Alistipes sp910575495	78.7172	96	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	99.23	98.47	0.95	0.90	3	-
GCF_000321205.1	s__Alistipes_A ihumii	78.6727	340	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.03	98.23	0.96	0.93	6	-
GCA_910583985.1	s__Alistipes_A sp910583985	78.6423	322	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900083545.1	s__Alistipes provencensis	78.3234	122	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	1.00	1.00	2	-
GCA_900549685.1	s__Alistipes_A sp900549685	78.2734	268	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210575.1	s__Alistipes shahii	77.9599	129	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.59	98.01	0.85	0.77	20	-
GCF_000231275.1	s__Alistipes_A indistinctus	77.8626	226	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	99.29	99.01	0.94	0.90	8	-
GCA_900546005.1	s__Alistipes_A pullicola	77.5026	233	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	97.97	97.84	0.94	0.92	3	-
GCA_019119305.1	s__Alistipes_A merdigallinarum	77.4289	233	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577475.1	s__Alistipes sp910577475	76.4888	86	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584485.1	s__Alistipes sp910584485	76.4011	83	954	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:15,249] [INFO] GTDB search result was written to GCF_014288115.1_ASM1428811v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:15,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:15,253] [INFO] DFAST_QC result json was written to GCF_014288115.1_ASM1428811v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:15,254] [INFO] DFAST_QC completed!
[2024-01-24 12:38:15,254] [INFO] Total running time: 0h1m17s