[2023-06-30 14:54:14,442] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:54:14,449] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:54:14,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference
[2023-06-30 14:54:15,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:54:15,907] [INFO] Task started: Prodigal
[2023-06-30 14:54:15,907] [INFO] Running command: gunzip -c /var/lib/cwl/stg73c45a7d-c303-4c38-bdca-5176e8204288/GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna.gz | prodigal -d GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/cds.fna -a GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:54:24,778] [INFO] Task succeeded: Prodigal
[2023-06-30 14:54:24,779] [INFO] Task started: HMMsearch
[2023-06-30 14:54:24,779] [INFO] Running command: hmmsearch --tblout GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/reference_markers.hmm GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:54:25,057] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:54:25,059] [INFO] Found 6/6 markers.
[2023-06-30 14:54:25,093] [INFO] Query marker FASTA was written to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/markers.fasta
[2023-06-30 14:54:25,093] [INFO] Task started: Blastn
[2023-06-30 14:54:25,094] [INFO] Running command: blastn -query GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/markers.fasta -db /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/reference_markers.fasta -out GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:54:25,824] [INFO] Task succeeded: Blastn
[2023-06-30 14:54:25,830] [INFO] Selected 31 target genomes.
[2023-06-30 14:54:25,830] [INFO] Target genome list was writen to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/target_genomes.txt
[2023-06-30 14:54:25,859] [INFO] Task started: fastANI
[2023-06-30 14:54:25,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c45a7d-c303-4c38-bdca-5176e8204288/GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna.gz --refList GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/target_genomes.txt --output GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:54:47,115] [INFO] Task succeeded: fastANI
[2023-06-30 14:54:47,115] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:54:47,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:54:47,117] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:54:47,117] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:54:47,118] [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 14:54:47,119] [INFO] DFAST Taxonomy check result was written to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/tc_result.tsv
[2023-06-30 14:54:47,120] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:54:47,120] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:54:47,120] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/checkm_data
[2023-06-30 14:54:47,123] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:54:47,161] [INFO] Task started: CheckM
[2023-06-30 14:54:47,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/checkm_input GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/checkm_result
[2023-06-30 14:55:17,238] [INFO] Task succeeded: CheckM
[2023-06-30 14:55:17,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 8.71%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-30 14:55:17,265] [INFO] ===== Completeness check finished =====
[2023-06-30 14:55:17,265] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:55:17,266] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/markers.fasta)
[2023-06-30 14:55:17,266] [INFO] Task started: Blastn
[2023-06-30 14:55:17,266] [INFO] Running command: blastn -query GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/markers.fasta -db /var/lib/cwl/stg825fcff1-c843-4d6c-a428-896dad3c7974/dqc_reference/reference_markers_gtdb.fasta -out GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:55:18,100] [INFO] Task succeeded: Blastn
[2023-06-30 14:55:18,103] [INFO] Selected 15 target genomes.
[2023-06-30 14:55:18,104] [INFO] Target genome list was writen to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:55:18,110] [INFO] Task started: fastANI
[2023-06-30 14:55:18,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg73c45a7d-c303-4c38-bdca-5176e8204288/GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna.gz --refList GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/target_genomes_gtdb.txt --output GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:55:25,869] [INFO] Task succeeded: fastANI
[2023-06-30 14:55:25,878] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:55:25,879] [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_903829085.1	s__UBA877 sp903829085	100.0	854	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017882065.1	s__UBA877 sp017882065	80.0693	270	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903884265.1	s__UBA877 sp903884265	80.0254	165	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	99.41	99.41	0.88	0.88	2	-
GCA_903873975.1	s__UBA877 sp903873975	79.6282	388	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882125.1	s__UBA877 sp017882125	77.9148	209	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009772985.1	s__UBA877 sp009772985	77.6579	162	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016934715.1	s__JAFGSI01 sp016934715	76.9535	111	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__JAFGSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001872165.1	s__CG2-30-58-95 sp001872165	76.9412	61	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__CG2-30-58-95	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882145.1	s__UBA877 sp017882145	76.8513	146	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016208355.1	s__UBA877 sp016208355	76.754	157	868	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA877	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:55:25,881] [INFO] GTDB search result was written to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/result_gtdb.tsv
[2023-06-30 14:55:25,881] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:55:25,884] [INFO] DFAST_QC result json was written to GCA_903829085.1_freshwater_MAG_---_AlinenSedimentsD0_bin-0676_genomic.fna/dqc_result.json
[2023-06-30 14:55:25,884] [INFO] DFAST_QC completed!
[2023-06-30 14:55:25,884] [INFO] Total running time: 0h1m11s