[2023-06-30 06:10:54,570] [INFO] DFAST_QC pipeline started.
[2023-06-30 06:10:54,574] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 06:10:54,574] [INFO] DQC Reference Directory: /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference
[2023-06-30 06:10:55,999] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 06:10:56,000] [INFO] Task started: Prodigal
[2023-06-30 06:10:56,000] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4e780a5-07c2-4c3e-87cd-43d75d2c61bb/GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna.gz | prodigal -d GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/cds.fna -a GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 06:11:04,439] [INFO] Task succeeded: Prodigal
[2023-06-30 06:11:04,439] [INFO] Task started: HMMsearch
[2023-06-30 06:11:04,440] [INFO] Running command: hmmsearch --tblout GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/reference_markers.hmm GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/protein.faa > /dev/null
[2023-06-30 06:11:04,618] [INFO] Task succeeded: HMMsearch
[2023-06-30 06:11:04,619] [INFO] Found 6/6 markers.
[2023-06-30 06:11:04,643] [INFO] Query marker FASTA was written to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/markers.fasta
[2023-06-30 06:11:04,643] [INFO] Task started: Blastn
[2023-06-30 06:11:04,644] [INFO] Running command: blastn -query GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/reference_markers.fasta -out GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:05,208] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:05,212] [INFO] Selected 27 target genomes.
[2023-06-30 06:11:05,212] [INFO] Target genome list was writen to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/target_genomes.txt
[2023-06-30 06:11:05,230] [INFO] Task started: fastANI
[2023-06-30 06:11:05,230] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e780a5-07c2-4c3e-87cd-43d75d2c61bb/GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna.gz --refList GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/target_genomes.txt --output GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 06:11:19,859] [INFO] Task succeeded: fastANI
[2023-06-30 06:11:19,859] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 06:11:19,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 06:11:19,861] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 06:11:19,861] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 06:11:19,861] [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 06:11:19,863] [INFO] DFAST Taxonomy check result was written to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/tc_result.tsv
[2023-06-30 06:11:19,863] [INFO] ===== Taxonomy check completed =====
[2023-06-30 06:11:19,863] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 06:11:19,864] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/checkm_data
[2023-06-30 06:11:19,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 06:11:19,893] [INFO] Task started: CheckM
[2023-06-30 06:11:19,894] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/checkm_input GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/checkm_result
[2023-06-30 06:11:48,922] [INFO] Task succeeded: CheckM
[2023-06-30 06:11:48,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 06:11:48,946] [INFO] ===== Completeness check finished =====
[2023-06-30 06:11:48,946] [INFO] ===== Start GTDB Search =====
[2023-06-30 06:11:48,946] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/markers.fasta)
[2023-06-30 06:11:48,947] [INFO] Task started: Blastn
[2023-06-30 06:11:48,947] [INFO] Running command: blastn -query GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/markers.fasta -db /var/lib/cwl/stg3b7122c1-f197-40dd-a2a6-110289542a3c/dqc_reference/reference_markers_gtdb.fasta -out GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 06:11:49,807] [INFO] Task succeeded: Blastn
[2023-06-30 06:11:49,810] [INFO] Selected 25 target genomes.
[2023-06-30 06:11:49,810] [INFO] Target genome list was writen to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 06:11:49,816] [INFO] Task started: fastANI
[2023-06-30 06:11:49,816] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4e780a5-07c2-4c3e-87cd-43d75d2c61bb/GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna.gz --refList GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/target_genomes_gtdb.txt --output GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 06:11:59,689] [INFO] Task succeeded: fastANI
[2023-06-30 06:11:59,693] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 06:11:59,693] [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_903939755.1	s__UBA952 sp903939755	99.9539	555	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	99.13	98.32	0.94	0.90	3	conclusive
GCA_018883325.1	s__UBA952 sp018883325	76.1103	50	569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Crocinitomicaceae;g__UBA952	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 06:11:59,695] [INFO] GTDB search result was written to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/result_gtdb.tsv
[2023-06-30 06:11:59,695] [INFO] ===== GTDB Search completed =====
[2023-06-30 06:11:59,698] [INFO] DFAST_QC result json was written to GCA_903951205.1_freshwater_MAG_---_Loc090519-5m_bin-0675_genomic.fna/dqc_result.json
[2023-06-30 06:11:59,698] [INFO] DFAST_QC completed!
[2023-06-30 06:11:59,698] [INFO] Total running time: 0h1m5s