[2023-06-28 00:28:12,046] [INFO] DFAST_QC pipeline started.
[2023-06-28 00:28:12,057] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 00:28:12,057] [INFO] DQC Reference Directory: /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference
[2023-06-28 00:28:13,561] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 00:28:13,562] [INFO] Task started: Prodigal
[2023-06-28 00:28:13,563] [INFO] Running command: gunzip -c /var/lib/cwl/stg01347d4b-911f-45c2-a87e-97d199764f1a/GCA_944321365.1_BRZ_PQ_bin90_genomic.fna.gz | prodigal -d GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/cds.fna -a GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 00:28:30,628] [INFO] Task succeeded: Prodigal
[2023-06-28 00:28:30,629] [INFO] Task started: HMMsearch
[2023-06-28 00:28:30,629] [INFO] Running command: hmmsearch --tblout GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/reference_markers.hmm GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/protein.faa > /dev/null
[2023-06-28 00:28:30,897] [INFO] Task succeeded: HMMsearch
[2023-06-28 00:28:30,899] [INFO] Found 6/6 markers.
[2023-06-28 00:28:30,938] [INFO] Query marker FASTA was written to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/markers.fasta
[2023-06-28 00:28:30,939] [INFO] Task started: Blastn
[2023-06-28 00:28:30,939] [INFO] Running command: blastn -query GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/reference_markers.fasta -out GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:28:31,572] [INFO] Task succeeded: Blastn
[2023-06-28 00:28:31,576] [INFO] Selected 30 target genomes.
[2023-06-28 00:28:31,576] [INFO] Target genome list was writen to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/target_genomes.txt
[2023-06-28 00:28:31,578] [INFO] Task started: fastANI
[2023-06-28 00:28:31,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg01347d4b-911f-45c2-a87e-97d199764f1a/GCA_944321365.1_BRZ_PQ_bin90_genomic.fna.gz --refList GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/target_genomes.txt --output GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 00:28:48,397] [INFO] Task succeeded: fastANI
[2023-06-28 00:28:48,398] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 00:28:48,398] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 00:28:48,413] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 00:28:48,414] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 00:28:48,414] [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
Paraprevotella xylaniphila	strain=YIT 11841	GCA_000205165.1	454155	454155	type	True	78.1115	340	899	95	below_threshold
Paraprevotella clara	strain=YIT 11840	GCA_000233955.1	454154	454154	type	True	78.102	335	899	95	below_threshold
Bacteroides zoogleoformans	strain=ATCC 33285	GCA_007830715.1	28119	28119	type	True	76.7693	66	899	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	76.7065	58	899	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	76.6671	59	899	95	below_threshold
Bacteroides humanifaecis	strain=KGMB07931	GCA_017309675.2	2792859	2792859	type	True	76.5748	65	899	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	76.4547	50	899	95	below_threshold
Bacteroides stercoris	strain=DSM 19555	GCA_900106605.1	46506	46506	suspected-type	True	76.3564	65	899	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_025147325.1	46506	46506	suspected-type	True	76.3309	67	899	95	below_threshold
Bacteroides stercoris	strain=ATCC 43183	GCA_000154525.1	46506	46506	suspected-type	True	76.3266	66	899	95	below_threshold
Phocaeicola coprophilus	strain=JCM 13818	GCA_001315785.1	387090	387090	type	True	76.272	57	899	95	below_threshold
Phocaeicola coprophilus	strain=DSM 18228	GCA_000157915.1	387090	387090	type	True	76.256	58	899	95	below_threshold
Phocaeicola barnesiae	strain=DSM 18169	GCA_000374585.1	376804	376804	type	True	76.2476	62	899	95	below_threshold
Bacteroides gallinarum	strain=DSM 18171	GCA_000374365.1	376806	376806	type	True	76.1734	65	899	95	below_threshold
Bacteroides gallinarum	strain=JCM 13658	GCA_000613665.1	376806	376806	type	True	76.1348	63	899	95	below_threshold
Bacteroides propionicigenes	strain=NSJ-90	GCA_018390535.1	2834112	2834112	type	True	76.1155	53	899	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.0786	53	899	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	75.7168	66	899	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 00:28:48,417] [INFO] DFAST Taxonomy check result was written to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/tc_result.tsv
[2023-06-28 00:28:48,418] [INFO] ===== Taxonomy check completed =====
[2023-06-28 00:28:48,418] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 00:28:48,418] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/checkm_data
[2023-06-28 00:28:48,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 00:28:48,463] [INFO] Task started: CheckM
[2023-06-28 00:28:48,463] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/checkm_input GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/checkm_result
[2023-06-28 00:29:37,870] [INFO] Task succeeded: CheckM
[2023-06-28 00:29:37,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 00:29:37,894] [INFO] ===== Completeness check finished =====
[2023-06-28 00:29:37,894] [INFO] ===== Start GTDB Search =====
[2023-06-28 00:29:37,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/markers.fasta)
[2023-06-28 00:29:37,895] [INFO] Task started: Blastn
[2023-06-28 00:29:37,895] [INFO] Running command: blastn -query GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/markers.fasta -db /var/lib/cwl/stgbc137712-f0b3-4a41-9cd7-1e799bb2db0b/dqc_reference/reference_markers_gtdb.fasta -out GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 00:29:38,779] [INFO] Task succeeded: Blastn
[2023-06-28 00:29:38,785] [INFO] Selected 17 target genomes.
[2023-06-28 00:29:38,785] [INFO] Target genome list was writen to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 00:29:38,805] [INFO] Task started: fastANI
[2023-06-28 00:29:38,806] [INFO] Running command: fastANI --query /var/lib/cwl/stg01347d4b-911f-45c2-a87e-97d199764f1a/GCA_944321365.1_BRZ_PQ_bin90_genomic.fna.gz --refList GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/target_genomes_gtdb.txt --output GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 00:29:48,662] [INFO] Task succeeded: fastANI
[2023-06-28 00:29:48,681] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 00:29:48,681] [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_000205165.1	s__Paraprevotella xylaniphila	78.1115	340	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.99	98.53	0.93	0.88	5	-
GCF_000233955.1	s__Paraprevotella clara	78.102	335	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	97.73	97.27	0.87	0.80	9	-
GCA_910586505.1	s__Paraprevotella sp910586505	77.8386	228	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548345.1	s__Paraprevotella sp900548345	77.6045	219	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900546665.1	s__Paraprevotella stercorigallinarum	77.3322	127	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	99.24	99.20	0.80	0.74	3	-
GCF_003477995.1	s__Paraprevotella sp003477995	77.2573	121	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	98.53	97.92	0.95	0.91	5	-
GCA_900760455.1	s__Paraprevotella sp900760455	77.2038	110	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	96.69	96.51	0.74	0.73	3	-
GCA_018883665.1	s__Paraprevotella stercoravium	77.098	89	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905215575.1	s__Paraprevotella sp905215575	76.6462	66	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Paraprevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004793475.1	s__Bacteroides sp002491635	76.4628	54	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.51	98.46	0.94	0.83	13	-
GCF_000374585.1	s__Phocaeicola barnesiae	76.3429	64	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.58	98.10	0.88	0.84	8	-
GCA_902362595.1	s__Phocaeicola merdigallinarum	76.2561	74	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	98.33	96.40	0.87	0.80	6	-
GCA_004558305.1	s__Phocaeicola plebeius_B	76.2287	76	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Phocaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374365.1	s__Bacteroides gallinarum	76.1734	65	899	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.97	99.97	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-28 00:29:48,685] [INFO] GTDB search result was written to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/result_gtdb.tsv
[2023-06-28 00:29:48,686] [INFO] ===== GTDB Search completed =====
[2023-06-28 00:29:48,691] [INFO] DFAST_QC result json was written to GCA_944321365.1_BRZ_PQ_bin90_genomic.fna/dqc_result.json
[2023-06-28 00:29:48,691] [INFO] DFAST_QC completed!
[2023-06-28 00:29:48,692] [INFO] Total running time: 0h1m37s