[2023-06-05 09:37:12,949] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:37:12,952] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:37:12,953] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference
[2023-06-05 09:37:15,965] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:37:15,967] [INFO] Task started: Prodigal
[2023-06-05 09:37:15,967] [INFO] Running command: gunzip -c /var/lib/cwl/stg8359596b-d9dc-40bd-a694-e97b57c2e9d5/GCA_934191335.1_ERR7745371_bin.47_genomic.fna.gz | prodigal -d GCA_934191335.1_ERR7745371_bin.47_genomic.fna/cds.fna -a GCA_934191335.1_ERR7745371_bin.47_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:37:32,468] [INFO] Task succeeded: Prodigal
[2023-06-05 09:37:32,469] [INFO] Task started: HMMsearch
[2023-06-05 09:37:32,469] [INFO] Running command: hmmsearch --tblout GCA_934191335.1_ERR7745371_bin.47_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/reference_markers.hmm GCA_934191335.1_ERR7745371_bin.47_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:37:32,719] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:37:32,721] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8359596b-d9dc-40bd-a694-e97b57c2e9d5/GCA_934191335.1_ERR7745371_bin.47_genomic.fna.gz]
[2023-06-05 09:37:32,752] [INFO] Query marker FASTA was written to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/markers.fasta
[2023-06-05 09:37:32,752] [INFO] Task started: Blastn
[2023-06-05 09:37:32,752] [INFO] Running command: blastn -query GCA_934191335.1_ERR7745371_bin.47_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/reference_markers.fasta -out GCA_934191335.1_ERR7745371_bin.47_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:33,353] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:33,357] [INFO] Selected 16 target genomes.
[2023-06-05 09:37:33,358] [INFO] Target genome list was writen to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/target_genomes.txt
[2023-06-05 09:37:33,359] [INFO] Task started: fastANI
[2023-06-05 09:37:33,359] [INFO] Running command: fastANI --query /var/lib/cwl/stg8359596b-d9dc-40bd-a694-e97b57c2e9d5/GCA_934191335.1_ERR7745371_bin.47_genomic.fna.gz --refList GCA_934191335.1_ERR7745371_bin.47_genomic.fna/target_genomes.txt --output GCA_934191335.1_ERR7745371_bin.47_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:37:40,764] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:40,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:37:40,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:37:40,776] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:37:40,777] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:37:40,777] [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
Prevotella pectinovora	strain=P4-76	GCA_000834015.1	1602169	1602169	type	True	79.2131	324	1032	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	77.5966	114	1032	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	77.5806	112	1032	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.4148	52	1032	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	77.3842	114	1032	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.8109	77	1032	95	below_threshold
Prevotella oris	strain=DSM 18711	GCA_000377685.1	28135	28135	type	True	76.7441	57	1032	95	below_threshold
Prevotella oris	strain=NCTC13071	GCA_900637655.1	28135	28135	type	True	76.7428	55	1032	95	below_threshold
Prevotella koreensis	strain=KCOM 3155	GCA_003977605.1	2490854	2490854	type	True	76.1714	68	1032	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:37:40,779] [INFO] DFAST Taxonomy check result was written to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/tc_result.tsv
[2023-06-05 09:37:40,780] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:37:40,780] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:37:40,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/checkm_data
[2023-06-05 09:37:40,783] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:37:40,824] [INFO] Task started: CheckM
[2023-06-05 09:37:40,824] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934191335.1_ERR7745371_bin.47_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934191335.1_ERR7745371_bin.47_genomic.fna/checkm_input GCA_934191335.1_ERR7745371_bin.47_genomic.fna/checkm_result
[2023-06-05 09:38:29,363] [INFO] Task succeeded: CheckM
[2023-06-05 09:38:29,365] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.53%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 09:38:29,385] [INFO] ===== Completeness check finished =====
[2023-06-05 09:38:29,385] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:38:29,386] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934191335.1_ERR7745371_bin.47_genomic.fna/markers.fasta)
[2023-06-05 09:38:29,386] [INFO] Task started: Blastn
[2023-06-05 09:38:29,386] [INFO] Running command: blastn -query GCA_934191335.1_ERR7745371_bin.47_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b7ae98a-272c-40ba-b3c6-aadb40eb46c2/dqc_reference/reference_markers_gtdb.fasta -out GCA_934191335.1_ERR7745371_bin.47_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:38:30,207] [INFO] Task succeeded: Blastn
[2023-06-05 09:38:30,211] [INFO] Selected 11 target genomes.
[2023-06-05 09:38:30,212] [INFO] Target genome list was writen to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:38:30,217] [INFO] Task started: fastANI
[2023-06-05 09:38:30,217] [INFO] Running command: fastANI --query /var/lib/cwl/stg8359596b-d9dc-40bd-a694-e97b57c2e9d5/GCA_934191335.1_ERR7745371_bin.47_genomic.fna.gz --refList GCA_934191335.1_ERR7745371_bin.47_genomic.fna/target_genomes_gtdb.txt --output GCA_934191335.1_ERR7745371_bin.47_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:38:36,182] [INFO] Task succeeded: fastANI
[2023-06-05 09:38:36,192] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:38:36,193] [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_002298545.1	s__Prevotella sp002298545	96.4776	700	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002314055.1	s__Prevotella sp002314055	93.3276	765	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.08	98.98	0.90	0.84	9	-
GCA_900557405.1	s__Prevotella sp900557405	79.7578	288	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.88	97.88	0.76	0.76	2	-
GCF_000834015.1	s__Prevotella pectinovora	79.169	327	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCA_900548745.1	s__Prevotella sp900548745	78.7026	316	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.94	97.91	0.83	0.71	3	-
GCA_900772835.1	s__Prevotella sp900772835	78.6395	275	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002251245.1	s__Prevotella sp002251245	77.1274	94	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.53	98.53	0.91	0.91	2	-
GCA_900545525.1	s__Prevotella sp900545525	76.8893	100	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	-
GCA_017415455.1	s__Prevotella sp017415455	76.8162	86	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_004557285.1	s__Prevotella sp004557285	76.5203	82	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_902800925.1	s__Prevotella sp902800925	75.5207	55	1032	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 09:38:36,195] [INFO] GTDB search result was written to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/result_gtdb.tsv
[2023-06-05 09:38:36,195] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:38:36,198] [INFO] DFAST_QC result json was written to GCA_934191335.1_ERR7745371_bin.47_genomic.fna/dqc_result.json
[2023-06-05 09:38:36,199] [INFO] DFAST_QC completed!
[2023-06-05 09:38:36,199] [INFO] Total running time: 0h1m23s