[2023-06-08 12:19:00,890] [INFO] DFAST_QC pipeline started.
[2023-06-08 12:19:00,892] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 12:19:00,892] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference
[2023-06-08 12:19:02,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 12:19:02,135] [INFO] Task started: Prodigal
[2023-06-08 12:19:02,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg74d85695-1cdd-4313-b4ed-4f435d8a28b7/GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 12:19:05,119] [INFO] Task succeeded: Prodigal
[2023-06-08 12:19:05,120] [INFO] Task started: HMMsearch
[2023-06-08 12:19:05,120] [INFO] Running command: hmmsearch --tblout GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/reference_markers.hmm GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 12:19:05,344] [INFO] Task succeeded: HMMsearch
[2023-06-08 12:19:05,346] [INFO] Found 6/6 markers.
[2023-06-08 12:19:05,368] [INFO] Query marker FASTA was written to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 12:19:05,369] [INFO] Task started: Blastn
[2023-06-08 12:19:05,369] [INFO] Running command: blastn -query GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/reference_markers.fasta -out GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:05,954] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:05,959] [INFO] Selected 18 target genomes.
[2023-06-08 12:19:05,959] [INFO] Target genome list was writen to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 12:19:05,966] [INFO] Task started: fastANI
[2023-06-08 12:19:05,966] [INFO] Running command: fastANI --query /var/lib/cwl/stg74d85695-1cdd-4313-b4ed-4f435d8a28b7/GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 12:19:14,413] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:14,414] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 12:19:14,414] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 12:19:14,416] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 12:19:14,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 12:19:14,416] [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 12:19:14,418] [INFO] DFAST Taxonomy check result was written to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 12:19:14,419] [INFO] ===== Taxonomy check completed =====
[2023-06-08 12:19:14,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 12:19:14,419] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/checkm_data
[2023-06-08 12:19:14,422] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 12:19:14,447] [INFO] Task started: CheckM
[2023-06-08 12:19:14,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 12:19:31,409] [INFO] Task succeeded: CheckM
[2023-06-08 12:19:31,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 12:19:31,432] [INFO] ===== Completeness check finished =====
[2023-06-08 12:19:31,432] [INFO] ===== Start GTDB Search =====
[2023-06-08 12:19:31,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 12:19:31,433] [INFO] Task started: Blastn
[2023-06-08 12:19:31,433] [INFO] Running command: blastn -query GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8e8cbe3-883a-449a-8bdf-91ac43a7a6d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 12:19:32,262] [INFO] Task succeeded: Blastn
[2023-06-08 12:19:32,267] [INFO] Selected 13 target genomes.
[2023-06-08 12:19:32,267] [INFO] Target genome list was writen to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 12:19:32,274] [INFO] Task started: fastANI
[2023-06-08 12:19:32,274] [INFO] Running command: fastANI --query /var/lib/cwl/stg74d85695-1cdd-4313-b4ed-4f435d8a28b7/GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 12:19:36,994] [INFO] Task succeeded: fastANI
[2023-06-08 12:19:37,012] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 12:19:37,012] [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_004558955.1	s__Zag111 sp004558955	79.0606	222	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.49	98.49	0.77	0.77	2	-
GCA_900551965.1	s__Zag111 sp900551965	78.4517	156	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584405.1	s__Zag111 sp910584405	78.3285	192	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405805.1	s__Zag111 sp002405805	78.1838	191	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002103105.1	s__Zag111 sp002103105	78.0919	147	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	97.50	95.26	0.92	0.84	7	-
GCA_002438405.1	s__Zag111 sp002438405	77.9881	161	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	99.96	99.93	0.99	0.98	3	-
GCA_014803505.1	s__Zag111 sp014803505	77.8883	129	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003258735.1	s__Zag111 sp003258735	77.8615	174	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	98.31	98.12	0.91	0.82	5	-
GCA_017626055.1	s__Zag111 sp017626055	77.8182	140	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015152555.1	s__Zag111 sp015152555	77.6327	127	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472545.1	s__Zag111 sp017472545	77.493	115	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794035.1	s__UBA2813 sp902794035	77.1531	87	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777855.1	s__UBA2813 sp902777855	77.0157	109	455	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 12:19:37,014] [INFO] GTDB search result was written to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 12:19:37,016] [INFO] ===== GTDB Search completed =====
[2023-06-08 12:19:37,018] [INFO] DFAST_QC result json was written to GCA_945833895.1_SRR5666658_bin.8_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 12:19:37,018] [INFO] DFAST_QC completed!
[2023-06-08 12:19:37,018] [INFO] Total running time: 0h0m36s