[2023-06-08 05:33:41,323] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:41,326] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:41,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference
[2023-06-08 05:33:42,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:42,587] [INFO] Task started: Prodigal
[2023-06-08 05:33:42,588] [INFO] Running command: gunzip -c /var/lib/cwl/stgee8a793a-40ed-4032-9784-019e8c1ccf78/GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:33:54,423] [INFO] Task succeeded: Prodigal
[2023-06-08 05:33:54,424] [INFO] Task started: HMMsearch
[2023-06-08 05:33:54,424] [INFO] Running command: hmmsearch --tblout GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/reference_markers.hmm GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:33:54,690] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:33:54,720] [INFO] Found 6/6 markers.
[2023-06-08 05:33:54,760] [INFO] Query marker FASTA was written to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 05:33:54,760] [INFO] Task started: Blastn
[2023-06-08 05:33:54,760] [INFO] Running command: blastn -query GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/reference_markers.fasta -out GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:55,509] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:55,513] [INFO] Selected 20 target genomes.
[2023-06-08 05:33:55,513] [INFO] Target genome list was writen to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 05:33:55,515] [INFO] Task started: fastANI
[2023-06-08 05:33:55,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8a793a-40ed-4032-9784-019e8c1ccf78/GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:34:06,742] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:06,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:34:06,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:34:06,758] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:34:06,758] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:34:06,758] [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=DSM 15922	GCA_000427365.1	28139	28139	type	True	79.1123	351	644	95	below_threshold
Rikenella microfusus	strain=NCTC11190	GCA_900455755.1	28139	28139	type	True	79.0494	360	644	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.4656	65	644	95	below_threshold
Alistipes senegalensis	strain=FDAARGOS_1578	GCA_020735725.1	1288121	1288121	type	True	76.4047	56	644	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.4047	56	644	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_000312145.1	1288121	1288121	type	True	76.4047	56	644	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_000231275.1	626932	626932	type	True	76.2932	52	644	95	below_threshold
Alistipes indistinctus	strain=YIT 12060	GCA_025144995.1	626932	626932	type	True	76.2932	52	644	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.2915	60	644	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	76.203	64	644	95	below_threshold
Alistipes onderdonkii subsp. vulgaris	strain=3BBH6	GCA_006542645.1	2585117	328813	type	True	76.0424	55	644	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:34:06,761] [INFO] DFAST Taxonomy check result was written to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 05:34:06,761] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:34:06,761] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:34:06,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/checkm_data
[2023-06-08 05:34:06,763] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:34:06,792] [INFO] Task started: CheckM
[2023-06-08 05:34:06,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 05:34:42,310] [INFO] Task succeeded: CheckM
[2023-06-08 05:34:42,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:34:42,340] [INFO] ===== Completeness check finished =====
[2023-06-08 05:34:42,340] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:34:42,341] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 05:34:42,341] [INFO] Task started: Blastn
[2023-06-08 05:34:42,341] [INFO] Running command: blastn -query GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6351c172-d7a3-452e-925a-867d1d893874/dqc_reference/reference_markers_gtdb.fasta -out GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:34:43,280] [INFO] Task succeeded: Blastn
[2023-06-08 05:34:43,285] [INFO] Selected 15 target genomes.
[2023-06-08 05:34:43,285] [INFO] Target genome list was writen to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:34:43,288] [INFO] Task started: fastANI
[2023-06-08 05:34:43,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgee8a793a-40ed-4032-9784-019e8c1ccf78/GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:34:54,255] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:54,270] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:34:54,271] [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_910579375.1	s__Rikenella sp910579375	97.1107	535	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910577125.1	s__Rikenella sp910577125	89.2732	516	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577885.1	s__Rikenella sp910577885	80.0468	323	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427365.1	s__Rikenella microfusus	79.0443	354	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900104655.1	s__Rikenella massiliensis	78.6477	273	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113395.1	s__Rikenella faecigallinarum	77.7877	226	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Rikenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312145.1	s__Alistipes senegalensis	76.4047	56	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.29	97.35	0.84	0.66	10	-
GCF_000265365.1	s__Alistipes finegoldii	76.2915	60	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.50	97.54	0.87	0.79	15	-
GCA_014982715.1	s__DSM-108975 sp014982715	76.2112	65	644	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:34:54,272] [INFO] GTDB search result was written to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 05:34:54,273] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:34:54,278] [INFO] DFAST_QC result json was written to GCA_947347595.1_SRR14698349_bin.16_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 05:34:54,278] [INFO] DFAST_QC completed!
[2023-06-08 05:34:54,278] [INFO] Total running time: 0h1m13s