[2023-06-08 12:44:45,763] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:44:45,766] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:44:45,766] [INFO] DQC Reference Directory: /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference
[2023-06-08 12:44:48,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:44:48,034] [INFO] Task started: Prodigal
[2023-06-08 12:44:48,034] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d811eb-a468-4b18-9edc-ce3066fc90db/GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:44:53,418] [INFO] Task succeeded: Prodigal
[2023-06-08 12:44:53,419] [INFO] Task started: HMMsearch
[2023-06-08 12:44:53,419] [INFO] Running command: hmmsearch --tblout GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/reference_markers.hmm GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:44:53,630] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:44:53,631] [INFO] Found 6/6 markers.
[2023-06-08 12:44:53,654] [INFO] Query marker FASTA was written to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:44:53,655] [INFO] Task started: Blastn
[2023-06-08 12:44:53,655] [INFO] Running command: blastn -query GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/reference_markers.fasta -out GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:44:54,304] [INFO] Task succeeded: Blastn
[2023-06-08 12:44:54,309] [INFO] Selected 21 target genomes.
[2023-06-08 12:44:54,310] [INFO] Target genome list was writen to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:44:54,314] [INFO] Task started: fastANI
[2023-06-08 12:44:54,314] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d811eb-a468-4b18-9edc-ce3066fc90db/GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:45:04,382] [INFO] Task succeeded: fastANI
[2023-06-08 12:45:04,383] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:45:04,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:45:04,390] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:45:04,390] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 12:45:04,390] [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
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.7389	53	620	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.728	52	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 12:45:04,393] [INFO] DFAST Taxonomy check result was written to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:45:04,393] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:45:04,393] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:45:04,394] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/checkm_data
[2023-06-08 12:45:04,395] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:45:04,422] [INFO] Task started: CheckM
[2023-06-08 12:45:04,422] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:45:26,412] [INFO] Task succeeded: CheckM
[2023-06-08 12:45:26,413] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:45:26,434] [INFO] ===== Completeness check finished =====
[2023-06-08 12:45:26,434] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:45:26,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:45:26,435] [INFO] Task started: Blastn
[2023-06-08 12:45:26,435] [INFO] Running command: blastn -query GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg043ce510-5272-47c6-b82d-08747a468347/dqc_reference/reference_markers_gtdb.fasta -out GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:45:27,559] [INFO] Task succeeded: Blastn
[2023-06-08 12:45:27,564] [INFO] Selected 25 target genomes.
[2023-06-08 12:45:27,564] [INFO] Target genome list was writen to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:45:27,572] [INFO] Task started: fastANI
[2023-06-08 12:45:27,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d811eb-a468-4b18-9edc-ce3066fc90db/GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:45:36,227] [INFO] Task succeeded: fastANI
[2023-06-08 12:45:36,251] [INFO] Found 23 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 12:45:36,251] [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_910589155.1	s__Faecousia sp910589155	98.6917	580	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900544975.1	s__Faecousia sp900544975	77.9734	110	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.46	99.22	0.93	0.93	4	-
GCA_015067545.1	s__Faecousia sp015067545	77.8756	59	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015067835.1	s__Faecousia sp015067835	77.8137	52	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004562395.1	s__Faecousia sp004562395	77.8086	64	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715835.1	s__Faecousia intestinavium	77.8084	65	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918045.1	s__Faecousia sp018918045	77.8064	73	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544405.1	s__Faecousia sp900544405	77.6636	89	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	97.57	97.43	0.89	0.88	3	-
GCA_018715805.1	s__Faecousia intestinigallinarum	77.6236	98	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713285.1	s__Faecousia excrementigallinarum	77.5165	86	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018712145.1	s__Faecousia faecigallinarum	77.4289	102	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900544945.1	s__Faecousia sp900544945	77.4232	82	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.60	96.52	0.82	0.81	4	-
GCA_900545515.1	s__Faecousia sp000435995	77.3914	121	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.49	98.99	0.94	0.88	3	-
GCA_002436765.1	s__Faecousia sp002436765	77.3653	87	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.53	99.53	0.91	0.91	2	-
GCA_017506735.1	s__Faecousia sp017506735	77.3635	60	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905205195.1	s__Faecousia sp900762935	77.3112	97	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.08	99.08	0.92	0.92	2	-
GCA_900549705.1	s__Faecousia sp900549705	77.2215	70	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	96.98	96.52	0.84	0.77	3	-
GCA_017622295.1	s__Faecousia sp017622295	77.1689	51	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068165.1	s__Faecousia sp015068165	77.0618	52	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004555705.1	s__Faecousia sp004555705	77.0437	73	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017416325.1	s__Faecousia sp017416325	76.9489	54	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437585.1	s__Faecousia sp002437585	76.9306	94	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	99.35	99.16	0.96	0.95	3	-
GCA_900556935.1	s__Faecousia sp900556935	76.6578	63	620	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Faecousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:45:36,253] [INFO] GTDB search result was written to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:45:36,253] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:45:36,257] [INFO] DFAST_QC result json was written to GCA_947643215.1_SRR15730529_bin.36_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:45:36,257] [INFO] DFAST_QC completed!
[2023-06-08 12:45:36,257] [INFO] Total running time: 0h0m50s