[2023-06-17 12:24:27,474] [INFO] DFAST_QC pipeline started.
[2023-06-17 12:24:27,476] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 12:24:27,476] [INFO] DQC Reference Directory: /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference
[2023-06-17 12:24:30,171] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 12:24:30,172] [INFO] Task started: Prodigal
[2023-06-17 12:24:30,172] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc3fb121-4793-459d-ad4f-5fa11f04a95b/GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna.gz | prodigal -d GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/cds.fna -a GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 12:24:34,044] [INFO] Task succeeded: Prodigal
[2023-06-17 12:24:34,045] [INFO] Task started: HMMsearch
[2023-06-17 12:24:34,045] [INFO] Running command: hmmsearch --tblout GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/reference_markers.hmm GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/protein.faa > /dev/null
[2023-06-17 12:24:34,180] [INFO] Task succeeded: HMMsearch
[2023-06-17 12:24:34,181] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfc3fb121-4793-459d-ad4f-5fa11f04a95b/GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna.gz]
[2023-06-17 12:24:34,203] [INFO] Query marker FASTA was written to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/markers.fasta
[2023-06-17 12:24:34,204] [INFO] Task started: Blastn
[2023-06-17 12:24:34,204] [INFO] Running command: blastn -query GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/markers.fasta -db /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/reference_markers.fasta -out GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:34,768] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:34,771] [INFO] Selected 7 target genomes.
[2023-06-17 12:24:34,772] [INFO] Target genome list was writen to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/target_genomes.txt
[2023-06-17 12:24:34,772] [INFO] Task started: fastANI
[2023-06-17 12:24:34,772] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3fb121-4793-459d-ad4f-5fa11f04a95b/GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna.gz --refList GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/target_genomes.txt --output GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 12:24:37,989] [INFO] Task succeeded: fastANI
[2023-06-17 12:24:37,989] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 12:24:37,990] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 12:24:37,996] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 12:24:37,997] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 12:24:37,997] [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
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	87.0112	328	425	95	below_threshold
Pusillibacter faecalis	strain=MM59	GCA_018408705.1	2714358	2714358	type	True	79.497	144	425	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	79.2035	130	425	95	below_threshold
Vescimonas coprocola	strain=MM50	GCA_018408575.1	2714355	2714355	type	True	78.4597	95	425	95	below_threshold
Oscillibacter ruminantium	strain=GH1	GCA_000307265.1	1263547	1263547	type	True	78.0609	108	425	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 12:24:37,999] [INFO] DFAST Taxonomy check result was written to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/tc_result.tsv
[2023-06-17 12:24:37,999] [INFO] ===== Taxonomy check completed =====
[2023-06-17 12:24:38,000] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 12:24:38,000] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/checkm_data
[2023-06-17 12:24:38,001] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 12:24:38,020] [INFO] Task started: CheckM
[2023-06-17 12:24:38,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/checkm_input GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/checkm_result
[2023-06-17 12:24:55,675] [INFO] Task succeeded: CheckM
[2023-06-17 12:24:55,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.06%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 12:24:55,697] [INFO] ===== Completeness check finished =====
[2023-06-17 12:24:55,698] [INFO] ===== Start GTDB Search =====
[2023-06-17 12:24:55,698] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/markers.fasta)
[2023-06-17 12:24:55,698] [INFO] Task started: Blastn
[2023-06-17 12:24:55,698] [INFO] Running command: blastn -query GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/markers.fasta -db /var/lib/cwl/stg964f4dac-4bea-459c-8da5-f214269271bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 12:24:56,447] [INFO] Task succeeded: Blastn
[2023-06-17 12:24:56,451] [INFO] Selected 6 target genomes.
[2023-06-17 12:24:56,451] [INFO] Target genome list was writen to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 12:24:56,454] [INFO] Task started: fastANI
[2023-06-17 12:24:56,454] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc3fb121-4793-459d-ad4f-5fa11f04a95b/GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna.gz --refList GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/target_genomes_gtdb.txt --output GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 12:25:00,061] [INFO] Task succeeded: fastANI
[2023-06-17 12:25:00,068] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 12:25:00,068] [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_016902445.1	s__Dysosmobacter avistercoris	97.9026	384	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.12	97.84	0.91	0.85	7	conclusive
GCA_019118245.1	s__Dysosmobacter excrementigallinarum	89.239	309	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118935.1	s__Dysosmobacter pullicola	88.7304	301	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.04	97.82	0.81	0.80	3	-
GCA_019118505.1	s__Dysosmobacter excrementavium	88.4558	292	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005121165.2	s__Dysosmobacter welbionis	86.9804	329	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	98.82	98.27	0.84	0.73	10	-
GCF_018228705.1	s__Dysosmobacter sp018228705	83.2832	266	425	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Dysosmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 12:25:00,070] [INFO] GTDB search result was written to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/result_gtdb.tsv
[2023-06-17 12:25:00,071] [INFO] ===== GTDB Search completed =====
[2023-06-17 12:25:00,074] [INFO] DFAST_QC result json was written to GCA_905202345.1_ERR1190619-mag-bin.36_genomic.fna/dqc_result.json
[2023-06-17 12:25:00,074] [INFO] DFAST_QC completed!
[2023-06-17 12:25:00,074] [INFO] Total running time: 0h0m33s