[2023-06-13 08:51:49,703] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:51:49,706] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:51:49,706] [INFO] DQC Reference Directory: /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference
[2023-06-13 08:51:51,506] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:51:51,507] [INFO] Task started: Prodigal
[2023-06-13 08:51:51,507] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b4d0826-eeba-44c6-b2eb-7f65cb5c7b80/GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:02,614] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:02,615] [INFO] Task started: HMMsearch
[2023-06-13 08:52:02,615] [INFO] Running command: hmmsearch --tblout GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/reference_markers.hmm GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:02,828] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:02,829] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4b4d0826-eeba-44c6-b2eb-7f65cb5c7b80/GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 08:52:02,850] [INFO] Query marker FASTA was written to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 08:52:02,850] [INFO] Task started: Blastn
[2023-06-13 08:52:02,851] [INFO] Running command: blastn -query GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/reference_markers.fasta -out GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:03,420] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:03,424] [INFO] Selected 26 target genomes.
[2023-06-13 08:52:03,424] [INFO] Target genome list was writen to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 08:52:03,427] [INFO] Task started: fastANI
[2023-06-13 08:52:03,427] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b4d0826-eeba-44c6-b2eb-7f65cb5c7b80/GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:14,793] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:14,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:14,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:14,800] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:52:14,800] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:52:14,800] [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	77.2563	90	532	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	77.0951	64	532	95	below_threshold
Prevotella lascolaii	strain=khD1	GCA_900079775.1	1776379	1776379	type	True	77.0644	90	532	95	below_threshold
Xylanibacter rodentium	strain=PROD	GCA_013166575.1	2736289	2736289	type	True	76.9385	74	532	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.4255	53	532	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:14,802] [INFO] DFAST Taxonomy check result was written to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 08:52:14,803] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:14,803] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:14,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/checkm_data
[2023-06-13 08:52:14,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:14,826] [INFO] Task started: CheckM
[2023-06-13 08:52:14,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 08:52:49,265] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:49,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.26%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:49,280] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:49,281] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:49,281] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 08:52:49,281] [INFO] Task started: Blastn
[2023-06-13 08:52:49,281] [INFO] Running command: blastn -query GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8f38b03a-38aa-4a18-bb84-9a9c8ecb9502/dqc_reference/reference_markers_gtdb.fasta -out GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:50,032] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:50,036] [INFO] Selected 17 target genomes.
[2023-06-13 08:52:50,037] [INFO] Target genome list was writen to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:50,045] [INFO] Task started: fastANI
[2023-06-13 08:52:50,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b4d0826-eeba-44c6-b2eb-7f65cb5c7b80/GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:52:58,010] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:58,023] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:52:58,024] [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_900545525.1	s__Prevotella sp900545525	98.8058	496	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.81	98.33	0.87	0.76	5	conclusive
GCF_013166515.1	s__Prevotella sp013166515	86.1367	439	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.36	96.74	0.93	0.86	3	-
GCA_000433175.1	s__Prevotella sp000433175	77.5341	99	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.10	97.93	0.86	0.84	3	-
GCF_001275135.1	s__Prevotella rara	77.5267	130	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.17	97.70	0.90	0.86	7	-
GCF_000834015.1	s__Prevotella pectinovora	77.2563	90	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.37	97.34	0.86	0.79	12	-
GCF_013166545.1	s__Prevotella sp013166545	77.1409	69	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.93	99.88	0.98	0.97	6	-
GCF_016899855.1	s__Prevotella sp000436595	77.1023	86	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.00	97.50	0.84	0.81	5	-
GCF_900079775.1	s__Prevotella lascolaii	77.0644	90	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.26	98.20	0.94	0.92	5	-
GCA_900557405.1	s__Prevotella sp900557405	76.8886	79	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.88	97.88	0.76	0.76	2	-
GCA_905196835.1	s__Prevotella stercoripullorum	76.883	117	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.53	95.99	0.92	0.86	5	-
GCA_004557285.1	s__Prevotella sp004557285	76.8725	70	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.35	98.35	0.77	0.77	2	-
GCA_002490315.1	s__Prevotella sp002490315	76.8351	54	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017415455.1	s__Prevotella sp017415455	76.7125	79	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.31	98.11	0.83	0.82	3	-
GCA_002353525.1	s__Prevotella sp002353525	76.6745	50	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016899955.1	s__Prevotella sp900540415	76.6482	85	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.44	98.08	0.94	0.91	6	-
GCA_017471245.1	s__Prevotella sp017471245	76.6195	60	532	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.04	98.04	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-13 08:52:58,026] [INFO] GTDB search result was written to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 08:52:58,026] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:52:58,030] [INFO] DFAST_QC result json was written to GCA_947365445.1_SRR16350253_bin.2_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 08:52:58,030] [INFO] DFAST_QC completed!
[2023-06-13 08:52:58,030] [INFO] Total running time: 0h1m8s