[2023-06-08 19:01:11,571] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:01:11,574] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:01:11,574] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference
[2023-06-08 19:01:15,008] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:01:15,009] [INFO] Task started: Prodigal
[2023-06-08 19:01:15,009] [INFO] Running command: gunzip -c /var/lib/cwl/stg3431ccb2-6378-4edf-bdb8-d43269a07bb8/GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:01:17,529] [INFO] Task succeeded: Prodigal
[2023-06-08 19:01:17,529] [INFO] Task started: HMMsearch
[2023-06-08 19:01:17,529] [INFO] Running command: hmmsearch --tblout GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/reference_markers.hmm GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:01:17,764] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:01:17,768] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3431ccb2-6378-4edf-bdb8-d43269a07bb8/GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 19:01:17,791] [INFO] Query marker FASTA was written to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 19:01:17,792] [INFO] Task started: Blastn
[2023-06-08 19:01:17,792] [INFO] Running command: blastn -query GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/reference_markers.fasta -out GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:18,876] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:18,881] [INFO] Selected 25 target genomes.
[2023-06-08 19:01:18,882] [INFO] Target genome list was writen to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 19:01:18,933] [INFO] Task started: fastANI
[2023-06-08 19:01:18,933] [INFO] Running command: fastANI --query /var/lib/cwl/stg3431ccb2-6378-4edf-bdb8-d43269a07bb8/GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:01:30,438] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:30,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:01:30,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:01:30,441] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:01:30,441] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:01:30,441] [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 19:01:30,443] [INFO] DFAST Taxonomy check result was written to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 19:01:30,443] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:01:30,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:01:30,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/checkm_data
[2023-06-08 19:01:30,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:01:30,472] [INFO] Task started: CheckM
[2023-06-08 19:01:30,472] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 19:01:46,482] [INFO] Task succeeded: CheckM
[2023-06-08 19:01:46,483] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:01:46,505] [INFO] ===== Completeness check finished =====
[2023-06-08 19:01:46,506] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:01:46,506] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 19:01:46,507] [INFO] Task started: Blastn
[2023-06-08 19:01:46,507] [INFO] Running command: blastn -query GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7b01f72-1dc5-46a5-a7fe-da420357fee8/dqc_reference/reference_markers_gtdb.fasta -out GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:47,239] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:47,243] [INFO] Selected 14 target genomes.
[2023-06-08 19:01:47,243] [INFO] Target genome list was writen to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:01:47,248] [INFO] Task started: fastANI
[2023-06-08 19:01:47,249] [INFO] Running command: fastANI --query /var/lib/cwl/stg3431ccb2-6378-4edf-bdb8-d43269a07bb8/GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:01:51,120] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:51,129] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 19:01:51,130] [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_017626395.1	s__RGIG5622 sp017626395	81.1005	261	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017534305.1	s__RGIG5622 sp017534305	80.2066	213	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__RGIG5622	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554875.1	s__CAG-465 sp900554875	77.1739	67	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772475.1	s__CAG-465 sp900772475	77.0407	91	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433135.1	s__CAG-465 sp000433135	76.9817	91	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	98.44	98.40	0.85	0.84	3	-
GCA_905204915.1	s__CAG-465 sp905204915	76.7977	84	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000433755.1	s__CAG-465 sp000433755	76.7564	90	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-465;g__CAG-465	95.0	97.80	97.49	0.91	0.90	4	-
GCA_017456555.1	s__Scatovivens sp017456555	75.6644	59	528	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__TANB77;f__CAG-508;g__Scatovivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:01:51,132] [INFO] GTDB search result was written to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 19:01:51,132] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:01:51,135] [INFO] DFAST_QC result json was written to GCA_945936085.1_SRR11489789_bin.23_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 19:01:51,136] [INFO] DFAST_QC completed!
[2023-06-08 19:01:51,136] [INFO] Total running time: 0h0m40s