[2023-06-30 22:12:16,647] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:12:16,651] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:12:16,651] [INFO] DQC Reference Directory: /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference
[2023-06-30 22:12:19,722] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:12:19,722] [INFO] Task started: Prodigal
[2023-06-30 22:12:19,723] [INFO] Running command: gunzip -c /var/lib/cwl/stge060532d-8128-43de-a0ae-9d05707dc618/GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:12:24,257] [INFO] Task succeeded: Prodigal
[2023-06-30 22:12:24,257] [INFO] Task started: HMMsearch
[2023-06-30 22:12:24,258] [INFO] Running command: hmmsearch --tblout GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/reference_markers.hmm GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:12:24,432] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:12:24,433] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge060532d-8128-43de-a0ae-9d05707dc618/GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-30 22:12:24,455] [INFO] Query marker FASTA was written to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-30 22:12:24,456] [INFO] Task started: Blastn
[2023-06-30 22:12:24,456] [INFO] Running command: blastn -query GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/reference_markers.fasta -out GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:12:25,024] [INFO] Task succeeded: Blastn
[2023-06-30 22:12:25,030] [INFO] Selected 12 target genomes.
[2023-06-30 22:12:25,030] [INFO] Target genome list was writen to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-30 22:12:25,031] [INFO] Task started: fastANI
[2023-06-30 22:12:25,031] [INFO] Running command: fastANI --query /var/lib/cwl/stge060532d-8128-43de-a0ae-9d05707dc618/GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:12:29,972] [INFO] Task succeeded: fastANI
[2023-06-30 22:12:29,973] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:12:29,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:12:29,981] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:12:29,981] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 22:12:29,981] [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
Selenomonas ruminantium subsp. ruminantium	strain=ATCC 12561	GCA_000424065.1	114196	971	type	True	77.2647	131	483	95	below_threshold
Mitsuokella multacida	strain=DSM 20544	GCA_000155955.1	52226	52226	type	True	77.1396	114	483	95	below_threshold
Anaerovibrio slackiae	strain=WCA-693-APC-5D-A	GCA_009695585.1	2652309	2652309	type	True	77.1041	91	483	95	below_threshold
Mitsuokella jalaludinii	strain=DSM 13811	GCA_000702905.1	187979	187979	type	True	77.027	107	483	95	below_threshold
Selenomonas montiformis	strain=WCA-380-WT-3B3	GCA_009697385.1	2652285	2652285	type	True	76.4765	55	483	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000160495.1	69823	69823	neotype	True	76.0587	53	483	95	below_threshold
Selenomonas sputigena	strain=ATCC 35185	GCA_000208405.1	69823	69823	neotype	True	75.9908	55	483	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 22:12:29,984] [INFO] DFAST Taxonomy check result was written to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-30 22:12:29,984] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:12:29,985] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:12:29,985] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/checkm_data
[2023-06-30 22:12:29,986] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:12:30,006] [INFO] Task started: CheckM
[2023-06-30 22:12:30,007] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-30 22:12:49,165] [INFO] Task succeeded: CheckM
[2023-06-30 22:12:49,166] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:12:49,183] [INFO] ===== Completeness check finished =====
[2023-06-30 22:12:49,184] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:12:49,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-30 22:12:49,184] [INFO] Task started: Blastn
[2023-06-30 22:12:49,185] [INFO] Running command: blastn -query GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stge025aea3-900b-4cd7-8981-96ae463bb7bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:12:49,960] [INFO] Task succeeded: Blastn
[2023-06-30 22:12:49,964] [INFO] Selected 7 target genomes.
[2023-06-30 22:12:49,964] [INFO] Target genome list was writen to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:12:49,973] [INFO] Task started: fastANI
[2023-06-30 22:12:49,973] [INFO] Running command: fastANI --query /var/lib/cwl/stge060532d-8128-43de-a0ae-9d05707dc618/GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:12:53,996] [INFO] Task succeeded: fastANI
[2023-06-30 22:12:54,003] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:12:54,003] [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_017635515.1	s__Selenomonas_B sp017635515	98.1954	434	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902780915.1	s__Selenomonas_B ruminantium_B	90.1748	418	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	97.28	97.28	0.79	0.79	2	-
GCA_015058655.1	s__Selenomonas_B ruminantium_C	87.1155	393	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702545.1	s__Selenomonas_B ruminantium_A	85.6391	418	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	96.24	95.81	0.75	0.73	3	-
GCA_905234515.1	s__Selenomonas_B sp905234515	81.9162	302	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015058625.1	s__Selenomonas_A ruminantium_N	77.3315	156	483	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Selenomonadaceae;g__Selenomonas_A	95.0	96.40	96.40	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-30 22:12:54,006] [INFO] GTDB search result was written to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-30 22:12:54,007] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:12:54,010] [INFO] DFAST_QC result json was written to GCA_946405015.1_SRR12081301_bin.29_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-30 22:12:54,010] [INFO] DFAST_QC completed!
[2023-06-30 22:12:54,011] [INFO] Total running time: 0h0m37s