[2023-06-30 21:26:47,231] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:26:47,233] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:26:47,233] [INFO] DQC Reference Directory: /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference
[2023-06-30 21:26:48,497] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:26:48,498] [INFO] Task started: Prodigal
[2023-06-30 21:26:48,498] [INFO] Running command: gunzip -c /var/lib/cwl/stge1b25f02-1256-4315-ac45-a562d8720538/GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna.gz | prodigal -d GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/cds.fna -a GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:26:53,024] [INFO] Task succeeded: Prodigal
[2023-06-30 21:26:53,025] [INFO] Task started: HMMsearch
[2023-06-30 21:26:53,025] [INFO] Running command: hmmsearch --tblout GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/reference_markers.hmm GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:26:53,233] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:26:53,234] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge1b25f02-1256-4315-ac45-a562d8720538/GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna.gz]
[2023-06-30 21:26:53,263] [INFO] Query marker FASTA was written to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/markers.fasta
[2023-06-30 21:26:53,264] [INFO] Task started: Blastn
[2023-06-30 21:26:53,264] [INFO] Running command: blastn -query GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/markers.fasta -db /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/reference_markers.fasta -out GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:26:54,150] [INFO] Task succeeded: Blastn
[2023-06-30 21:26:54,155] [INFO] Selected 35 target genomes.
[2023-06-30 21:26:54,156] [INFO] Target genome list was writen to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/target_genomes.txt
[2023-06-30 21:26:54,162] [INFO] Task started: fastANI
[2023-06-30 21:26:54,163] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b25f02-1256-4315-ac45-a562d8720538/GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna.gz --refList GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/target_genomes.txt --output GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:27:20,429] [INFO] Task succeeded: fastANI
[2023-06-30 21:27:20,430] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:27:20,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:27:20,433] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:27:20,433] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:27:20,434] [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
--------------------------------------------------------------------------------
[2023-06-30 21:27:20,436] [INFO] DFAST Taxonomy check result was written to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/tc_result.tsv
[2023-06-30 21:27:20,437] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:27:20,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:27:20,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/checkm_data
[2023-06-30 21:27:20,442] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:27:20,467] [INFO] Task started: CheckM
[2023-06-30 21:27:20,467] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/checkm_input GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/checkm_result
[2023-06-30 21:27:40,391] [INFO] Task succeeded: CheckM
[2023-06-30 21:27:40,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.48%
Contamintation: 4.17%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-06-30 21:27:40,416] [INFO] ===== Completeness check finished =====
[2023-06-30 21:27:40,416] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:27:40,417] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/markers.fasta)
[2023-06-30 21:27:40,417] [INFO] Task started: Blastn
[2023-06-30 21:27:40,417] [INFO] Running command: blastn -query GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/markers.fasta -db /var/lib/cwl/stg166218d7-5bd9-4def-b00d-c014fc5b1576/dqc_reference/reference_markers_gtdb.fasta -out GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:27:41,891] [INFO] Task succeeded: Blastn
[2023-06-30 21:27:41,896] [INFO] Selected 12 target genomes.
[2023-06-30 21:27:41,897] [INFO] Target genome list was writen to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:27:41,906] [INFO] Task started: fastANI
[2023-06-30 21:27:41,906] [INFO] Running command: fastANI --query /var/lib/cwl/stge1b25f02-1256-4315-ac45-a562d8720538/GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna.gz --refList GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/target_genomes_gtdb.txt --output GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:27:49,113] [INFO] Task succeeded: fastANI
[2023-06-30 21:27:49,124] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 21:27:49,124] [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_903940375.1	s__UBA10649 sp903940375	97.9237	190	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.93	98.93	0.81	0.81	2	conclusive
GCA_903908025.1	s__UBA10649 sp903908025	84.9612	167	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	98.87	97.91	0.84	0.77	3	-
GCA_016717115.1	s__UBA10649 sp016717115	79.1607	117	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017856385.1	s__UBA10649 sp017856385	78.677	73	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016125355.1	s__UBA10649 sp016125355	78.6494	103	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017849335.1	s__UBA10649 sp017849335	78.6265	75	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003456155.1	s__UBA10649 sp003456155	78.5377	63	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903934925.1	s__UBA10649 sp903934925	78.4806	67	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__UBA10649	95.0	99.42	99.35	0.85	0.83	4	-
GCA_009699015.1	s__WLND01 sp009699015	77.6628	57	216	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__S36-B12;g__WLND01	95.0	98.95	98.95	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-30 21:27:49,126] [INFO] GTDB search result was written to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/result_gtdb.tsv
[2023-06-30 21:27:49,127] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:27:49,130] [INFO] DFAST_QC result json was written to GCA_903945535.1_freshwater_MAG_---_Loc090721-6m_bin-871_genomic.fna/dqc_result.json
[2023-06-30 21:27:49,130] [INFO] DFAST_QC completed!
[2023-06-30 21:27:49,130] [INFO] Total running time: 0h1m2s