[2023-06-08 13:33:27,051] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:33:27,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:33:27,052] [INFO] DQC Reference Directory: /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference
[2023-06-08 13:33:28,180] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:33:28,184] [INFO] Task started: Prodigal
[2023-06-08 13:33:28,184] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf874eb6-ede7-4fcd-93fc-0359cfa1bcf0/GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:33:31,229] [INFO] Task succeeded: Prodigal
[2023-06-08 13:33:31,229] [INFO] Task started: HMMsearch
[2023-06-08 13:33:31,229] [INFO] Running command: hmmsearch --tblout GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/reference_markers.hmm GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:33:31,402] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:33:31,403] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbf874eb6-ede7-4fcd-93fc-0359cfa1bcf0/GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 13:33:31,421] [INFO] Query marker FASTA was written to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 13:33:31,421] [INFO] Task started: Blastn
[2023-06-08 13:33:31,421] [INFO] Running command: blastn -query GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/reference_markers.fasta -out GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:31,924] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:31,927] [INFO] Selected 15 target genomes.
[2023-06-08 13:33:31,927] [INFO] Target genome list was writen to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 13:33:31,930] [INFO] Task started: fastANI
[2023-06-08 13:33:31,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf874eb6-ede7-4fcd-93fc-0359cfa1bcf0/GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:33:38,112] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:38,113] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:33:38,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:33:38,119] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:33:38,119] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:33:38,119] [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
Anaerovibrio slackiae	strain=WCA-693-APC-5D-A	GCA_009695585.1	2652309	2652309	type	True	79.979	178	433	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:33:38,121] [INFO] DFAST Taxonomy check result was written to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 13:33:38,121] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:33:38,121] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:33:38,121] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/checkm_data
[2023-06-08 13:33:38,122] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:33:38,142] [INFO] Task started: CheckM
[2023-06-08 13:33:38,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 13:33:53,255] [INFO] Task succeeded: CheckM
[2023-06-08 13:33:53,256] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:33:53,272] [INFO] ===== Completeness check finished =====
[2023-06-08 13:33:53,272] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:33:53,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 13:33:53,273] [INFO] Task started: Blastn
[2023-06-08 13:33:53,273] [INFO] Running command: blastn -query GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgda685eb3-ffc5-4b5c-9f36-e02121498621/dqc_reference/reference_markers_gtdb.fasta -out GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:33:53,944] [INFO] Task succeeded: Blastn
[2023-06-08 13:33:53,947] [INFO] Selected 12 target genomes.
[2023-06-08 13:33:53,947] [INFO] Target genome list was writen to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:33:53,955] [INFO] Task started: fastANI
[2023-06-08 13:33:53,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf874eb6-ede7-4fcd-93fc-0359cfa1bcf0/GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:33:58,251] [INFO] Task succeeded: fastANI
[2023-06-08 13:33:58,257] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:33:58,258] [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_900548165.1	s__Anaerovibrio sp900548165	95.9743	302	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	96.97	96.65	0.86	0.85	4	conclusive
GCF_009695585.1	s__Anaerovibrio slackiae	79.979	178	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	98.28	97.88	0.95	0.93	10	-
GCA_016302095.1	s__Anaerovibrio sp016302095	79.0787	106	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768695.1	s__Anaerovibrio sp900768695	78.4671	112	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621545.1	s__Anaerovibrio lipolyticus_A	78.1383	99	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785445.1	s__Anaerovibrio sp902785445	77.8479	66	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002372665.1	s__Anaerovibrio lipolyticus_C	77.8429	80	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	97.79	96.86	0.90	0.86	3	-
GCA_017390245.1	s__Anaerovibrio sp017390245	77.7995	98	433	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Anaerovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:33:58,260] [INFO] GTDB search result was written to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 13:33:58,260] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:33:58,285] [INFO] DFAST_QC result json was written to GCA_945873665.1_SRR17382096_bin.6_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 13:33:58,285] [INFO] DFAST_QC completed!
[2023-06-08 13:33:58,285] [INFO] Total running time: 0h0m31s