[2023-06-08 00:35:02,836] [INFO] DFAST_QC pipeline started.
[2023-06-08 00:35:02,839] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 00:35:02,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference
[2023-06-08 00:35:06,329] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 00:35:06,334] [INFO] Task started: Prodigal
[2023-06-08 00:35:06,334] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c78b680-7f4c-4cfc-a82e-3f2b09b0ef4c/GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 00:35:11,607] [INFO] Task succeeded: Prodigal
[2023-06-08 00:35:11,607] [INFO] Task started: HMMsearch
[2023-06-08 00:35:11,608] [INFO] Running command: hmmsearch --tblout GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/reference_markers.hmm GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 00:35:11,848] [INFO] Task succeeded: HMMsearch
[2023-06-08 00:35:11,849] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5c78b680-7f4c-4cfc-a82e-3f2b09b0ef4c/GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 00:35:11,901] [INFO] Query marker FASTA was written to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 00:35:11,902] [INFO] Task started: Blastn
[2023-06-08 00:35:11,902] [INFO] Running command: blastn -query GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/reference_markers.fasta -out GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:12,503] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:12,506] [INFO] Selected 20 target genomes.
[2023-06-08 00:35:12,507] [INFO] Target genome list was writen to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 00:35:12,511] [INFO] Task started: fastANI
[2023-06-08 00:35:12,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c78b680-7f4c-4cfc-a82e-3f2b09b0ef4c/GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 00:35:26,496] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:26,497] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 00:35:26,497] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 00:35:26,499] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 00:35:26,499] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 00:35:26,500] [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
--------------------------------------------------------------------------------
[2023-06-08 00:35:26,501] [INFO] DFAST Taxonomy check result was written to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 00:35:26,502] [INFO] ===== Taxonomy check completed =====
[2023-06-08 00:35:26,502] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 00:35:26,503] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/checkm_data
[2023-06-08 00:35:26,507] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 00:35:26,531] [INFO] Task started: CheckM
[2023-06-08 00:35:26,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 00:35:48,432] [INFO] Task succeeded: CheckM
[2023-06-08 00:35:48,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 64.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 00:35:48,455] [INFO] ===== Completeness check finished =====
[2023-06-08 00:35:48,455] [INFO] ===== Start GTDB Search =====
[2023-06-08 00:35:48,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 00:35:48,456] [INFO] Task started: Blastn
[2023-06-08 00:35:48,456] [INFO] Running command: blastn -query GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6636bdcc-d804-411b-a77c-4241cb34ebde/dqc_reference/reference_markers_gtdb.fasta -out GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 00:35:49,269] [INFO] Task succeeded: Blastn
[2023-06-08 00:35:49,273] [INFO] Selected 14 target genomes.
[2023-06-08 00:35:49,274] [INFO] Target genome list was writen to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 00:35:49,281] [INFO] Task started: fastANI
[2023-06-08 00:35:49,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c78b680-7f4c-4cfc-a82e-3f2b09b0ef4c/GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 00:35:55,859] [INFO] Task succeeded: fastANI
[2023-06-08 00:35:55,873] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 00:35:55,873] [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_900316415.1	s__RUG740 sp900316415	81.0598	302	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902778055.1	s__RUG740 sp902778055	80.5218	330	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	97.78	97.78	0.89	0.89	2	-
GCA_017469265.1	s__RUG740 sp017469265	80.1959	279	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017464305.1	s__RUG740 sp017464305	79.7612	180	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017470145.1	s__RUG740 sp017470145	79.6156	225	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412715.1	s__RUG740 sp017412715	79.4766	194	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017512805.1	s__RUG740 sp017512805	79.1821	227	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900321945.1	s__RUG740 sp900321945	78.8401	142	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	100.00	100.00	0.98	0.98	2	-
GCA_900315675.1	s__GCA-900199385 sp900315675	78.6973	156	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	98.62	97.73	0.95	0.88	5	-
GCA_902797445.1	s__RUG740 sp902797445	78.5949	173	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__RUG740	95.0	98.52	98.52	0.71	0.71	2	-
GCA_902764875.1	s__GCA-900199385 sp902764875	78.141	186	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__GCA-900199385	95.0	96.75	96.19	0.79	0.75	4	-
GCA_017513475.1	s__UBA11524 sp017513475	77.3701	63	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016295665.1	s__HGM11604 sp016295665	77.0844	97	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__HGM11604	95.0	98.69	98.69	0.84	0.84	2	-
GCA_017936765.1	s__UBA11524 sp017936765	76.9444	105	693	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-74;g__UBA11524	95.0	96.73	96.73	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2023-06-08 00:35:55,875] [INFO] GTDB search result was written to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 00:35:55,876] [INFO] ===== GTDB Search completed =====
[2023-06-08 00:35:55,879] [INFO] DFAST_QC result json was written to GCA_947166705.1_SRR8387714_bin.95_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 00:35:55,880] [INFO] DFAST_QC completed!
[2023-06-08 00:35:55,880] [INFO] Total running time: 0h0m53s