[2023-07-01 04:22:11,282] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:22:11,284] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:22:11,284] [INFO] DQC Reference Directory: /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference
[2023-07-01 04:22:13,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:22:13,411] [INFO] Task started: Prodigal
[2023-07-01 04:22:13,411] [INFO] Running command: gunzip -c /var/lib/cwl/stgac7422f8-c851-4c0c-b34d-6d392d379edc/GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna.gz | prodigal -d GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/cds.fna -a GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:22:20,862] [INFO] Task succeeded: Prodigal
[2023-07-01 04:22:20,863] [INFO] Task started: HMMsearch
[2023-07-01 04:22:20,863] [INFO] Running command: hmmsearch --tblout GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/reference_markers.hmm GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:22:21,123] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:22:21,124] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgac7422f8-c851-4c0c-b34d-6d392d379edc/GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna.gz]
[2023-07-01 04:22:21,154] [INFO] Query marker FASTA was written to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/markers.fasta
[2023-07-01 04:22:21,155] [INFO] Task started: Blastn
[2023-07-01 04:22:21,155] [INFO] Running command: blastn -query GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/markers.fasta -db /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/reference_markers.fasta -out GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:22:21,920] [INFO] Task succeeded: Blastn
[2023-07-01 04:22:21,924] [INFO] Selected 18 target genomes.
[2023-07-01 04:22:21,925] [INFO] Target genome list was writen to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/target_genomes.txt
[2023-07-01 04:22:21,930] [INFO] Task started: fastANI
[2023-07-01 04:22:21,931] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7422f8-c851-4c0c-b34d-6d392d379edc/GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna.gz --refList GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/target_genomes.txt --output GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:22:41,196] [INFO] Task succeeded: fastANI
[2023-07-01 04:22:41,197] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:22:41,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:22:41,200] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:22:41,200] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:22:41,200] [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
--------------------------------------------------------------------------------
[2023-07-01 04:22:41,202] [INFO] DFAST Taxonomy check result was written to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/tc_result.tsv
[2023-07-01 04:22:41,203] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:22:41,203] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:22:41,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/checkm_data
[2023-07-01 04:22:41,208] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:22:41,246] [INFO] Task started: CheckM
[2023-07-01 04:22:41,247] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/checkm_input GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/checkm_result
[2023-07-01 04:23:08,357] [INFO] Task succeeded: CheckM
[2023-07-01 04:23:08,359] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.38%
Contamintation: 6.48%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-07-01 04:23:08,383] [INFO] ===== Completeness check finished =====
[2023-07-01 04:23:08,383] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:23:08,384] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/markers.fasta)
[2023-07-01 04:23:08,384] [INFO] Task started: Blastn
[2023-07-01 04:23:08,384] [INFO] Running command: blastn -query GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/markers.fasta -db /var/lib/cwl/stg85488774-3090-49e2-b8de-e7eadae6c41d/dqc_reference/reference_markers_gtdb.fasta -out GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:23:08,945] [INFO] Task succeeded: Blastn
[2023-07-01 04:23:08,950] [INFO] Selected 6 target genomes.
[2023-07-01 04:23:08,950] [INFO] Target genome list was writen to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:23:08,954] [INFO] Task started: fastANI
[2023-07-01 04:23:08,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgac7422f8-c851-4c0c-b34d-6d392d379edc/GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna.gz --refList GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/target_genomes_gtdb.txt --output GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:23:15,433] [INFO] Task succeeded: fastANI
[2023-07-01 04:23:15,445] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:23:15,445] [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_903924465.1	s__CAIYBN01 sp903924465	99.5299	269	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903929795.1	s__CAIYBN01 sp903929795	81.1126	206	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.55	99.37	0.95	0.92	7	-
GCA_903869075.1	s__CAIYBN01 sp903869075	80.7377	183	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842345.1	s__CAIYBN01 sp903842345	80.3174	206	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.98	99.97	0.99	0.98	4	-
GCA_903850505.1	s__CAIYBN01 sp903850505	80.1035	197	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903896545.1	s__CAIYBN01 sp903896545	79.4266	180	278	d__Bacteria;p__Myxococcota;c__UBA9042;o__UBA9042;f__UBA9042;g__CAIYBN01	95.0	99.47	98.78	0.94	0.88	6	-
--------------------------------------------------------------------------------
[2023-07-01 04:23:15,448] [INFO] GTDB search result was written to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/result_gtdb.tsv
[2023-07-01 04:23:15,449] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:23:15,453] [INFO] DFAST_QC result json was written to GCA_903913755.1_freshwater_MAG_---_MJ110802A_bin-629_genomic.fna/dqc_result.json
[2023-07-01 04:23:15,453] [INFO] DFAST_QC completed!
[2023-07-01 04:23:15,453] [INFO] Total running time: 0h1m4s