[2023-06-28 08:21:39,366] [INFO] DFAST_QC pipeline started.
[2023-06-28 08:21:39,369] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 08:21:39,369] [INFO] DQC Reference Directory: /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference
[2023-06-28 08:21:40,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 08:21:40,592] [INFO] Task started: Prodigal
[2023-06-28 08:21:40,593] [INFO] Running command: gunzip -c /var/lib/cwl/stg12a32075-71ca-4dbd-8033-7ec7c4eef25f/GCA_944322065.1_BRZ_KV_bin62_genomic.fna.gz | prodigal -d GCA_944322065.1_BRZ_KV_bin62_genomic.fna/cds.fna -a GCA_944322065.1_BRZ_KV_bin62_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 08:21:57,280] [INFO] Task succeeded: Prodigal
[2023-06-28 08:21:57,281] [INFO] Task started: HMMsearch
[2023-06-28 08:21:57,281] [INFO] Running command: hmmsearch --tblout GCA_944322065.1_BRZ_KV_bin62_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/reference_markers.hmm GCA_944322065.1_BRZ_KV_bin62_genomic.fna/protein.faa > /dev/null
[2023-06-28 08:21:57,473] [INFO] Task succeeded: HMMsearch
[2023-06-28 08:21:57,474] [INFO] Found 6/6 markers.
[2023-06-28 08:21:57,498] [INFO] Query marker FASTA was written to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/markers.fasta
[2023-06-28 08:21:57,498] [INFO] Task started: Blastn
[2023-06-28 08:21:57,499] [INFO] Running command: blastn -query GCA_944322065.1_BRZ_KV_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/reference_markers.fasta -out GCA_944322065.1_BRZ_KV_bin62_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:21:58,153] [INFO] Task succeeded: Blastn
[2023-06-28 08:21:58,169] [INFO] Selected 28 target genomes.
[2023-06-28 08:21:58,170] [INFO] Target genome list was writen to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/target_genomes.txt
[2023-06-28 08:21:58,171] [INFO] Task started: fastANI
[2023-06-28 08:21:58,171] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a32075-71ca-4dbd-8033-7ec7c4eef25f/GCA_944322065.1_BRZ_KV_bin62_genomic.fna.gz --refList GCA_944322065.1_BRZ_KV_bin62_genomic.fna/target_genomes.txt --output GCA_944322065.1_BRZ_KV_bin62_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 08:22:15,304] [INFO] Task succeeded: fastANI
[2023-06-28 08:22:15,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 08:22:15,304] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 08:22:15,321] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 08:22:15,321] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 08:22:15,321] [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
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	77.4069	150	812	95	below_threshold
Bacteroides rodentium	strain=JCM 16496	GCA_000614125.1	691816	691816	type	True	77.3579	207	812	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	77.2961	153	812	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	77.2901	71	812	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	77.2854	155	812	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	77.253	187	812	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	77.2523	157	812	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_000154205.1	820	820	type	True	77.2517	189	812	95	below_threshold
Bacteroides uniformis	strain=FDAARGOS_901	GCA_016117815.1	820	820	type	True	77.2443	190	812	95	below_threshold
Bacteroides uniformis	strain=DSM 6597	GCA_900107315.1	820	820	type	True	77.2423	187	812	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	77.1799	191	812	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	77.1755	184	812	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	77.1681	186	812	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_000155815.1	28111	28111	type	True	76.8324	135	812	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	76.8272	131	812	95	below_threshold
Bacteroides eggerthii	strain=NCTC11155	GCA_900445565.1	28111	28111	type	True	76.8268	131	812	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	76.7891	123	812	95	below_threshold
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	76.6905	59	812	95	below_threshold
Phocaeicola intestinalis	strain=Sa1CVN1	GCA_014837065.1	2762212	2762212	type	True	76.6364	115	812	95	below_threshold
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	76.5735	90	812	95	below_threshold
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	76.4424	104	812	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.439	74	812	95	below_threshold
Prevotella mizrahii	strain=LKV-178-WT-2A	GCA_009695775.1	2606637	2606637	type	True	75.6721	52	812	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 08:22:15,323] [INFO] DFAST Taxonomy check result was written to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/tc_result.tsv
[2023-06-28 08:22:15,324] [INFO] ===== Taxonomy check completed =====
[2023-06-28 08:22:15,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 08:22:15,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/checkm_data
[2023-06-28 08:22:15,325] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 08:22:15,353] [INFO] Task started: CheckM
[2023-06-28 08:22:15,353] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944322065.1_BRZ_KV_bin62_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944322065.1_BRZ_KV_bin62_genomic.fna/checkm_input GCA_944322065.1_BRZ_KV_bin62_genomic.fna/checkm_result
[2023-06-28 08:23:01,720] [INFO] Task succeeded: CheckM
[2023-06-28 08:23:01,721] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 08:23:01,735] [INFO] ===== Completeness check finished =====
[2023-06-28 08:23:01,735] [INFO] ===== Start GTDB Search =====
[2023-06-28 08:23:01,736] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944322065.1_BRZ_KV_bin62_genomic.fna/markers.fasta)
[2023-06-28 08:23:01,736] [INFO] Task started: Blastn
[2023-06-28 08:23:01,736] [INFO] Running command: blastn -query GCA_944322065.1_BRZ_KV_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stg584b7a47-d36a-4b44-9441-c5d4a4e1930c/dqc_reference/reference_markers_gtdb.fasta -out GCA_944322065.1_BRZ_KV_bin62_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 08:23:02,816] [INFO] Task succeeded: Blastn
[2023-06-28 08:23:02,819] [INFO] Selected 7 target genomes.
[2023-06-28 08:23:02,819] [INFO] Target genome list was writen to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 08:23:02,821] [INFO] Task started: fastANI
[2023-06-28 08:23:02,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a32075-71ca-4dbd-8033-7ec7c4eef25f/GCA_944322065.1_BRZ_KV_bin62_genomic.fna.gz --refList GCA_944322065.1_BRZ_KV_bin62_genomic.fna/target_genomes_gtdb.txt --output GCA_944322065.1_BRZ_KV_bin62_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 08:23:07,216] [INFO] Task succeeded: fastANI
[2023-06-28 08:23:07,223] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 08:23:07,223] [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_019115825.1	s__Bacteroides pullicola	95.8847	652	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019116285.1	s__Bacteroides merdigallinarum	85.6719	509	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018883785.1	s__Bacteroides intestinipullorum	84.9115	526	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118325.1	s__Bacteroides intestinavium	83.8297	498	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002160055.1	s__Bacteroides avicola	79.4866	364	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.46	98.46	0.91	0.91	2	-
GCF_900128475.1	s__Bacteroides massiliensis	79.4509	340	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	97.63	97.57	0.90	0.85	6	-
GCA_019116805.1	s__Bacteroides merdavium	78.6931	248	812	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 08:23:07,225] [INFO] GTDB search result was written to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/result_gtdb.tsv
[2023-06-28 08:23:07,225] [INFO] ===== GTDB Search completed =====
[2023-06-28 08:23:07,229] [INFO] DFAST_QC result json was written to GCA_944322065.1_BRZ_KV_bin62_genomic.fna/dqc_result.json
[2023-06-28 08:23:07,229] [INFO] DFAST_QC completed!
[2023-06-28 08:23:07,229] [INFO] Total running time: 0h1m28s