[2023-06-30 20:54:50,613] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:54:50,617] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:54:50,618] [INFO] DQC Reference Directory: /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference
[2023-06-30 20:54:51,889] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:54:51,889] [INFO] Task started: Prodigal
[2023-06-30 20:54:51,890] [INFO] Running command: gunzip -c /var/lib/cwl/stgeac50242-e8be-4de8-a49d-a9877f7813c0/GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna.gz | prodigal -d GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/cds.fna -a GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:55:08,602] [INFO] Task succeeded: Prodigal
[2023-06-30 20:55:08,603] [INFO] Task started: HMMsearch
[2023-06-30 20:55:08,603] [INFO] Running command: hmmsearch --tblout GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/reference_markers.hmm GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:55:08,833] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:55:08,835] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgeac50242-e8be-4de8-a49d-a9877f7813c0/GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna.gz]
[2023-06-30 20:55:08,871] [INFO] Query marker FASTA was written to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/markers.fasta
[2023-06-30 20:55:08,872] [INFO] Task started: Blastn
[2023-06-30 20:55:08,872] [INFO] Running command: blastn -query GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/markers.fasta -db /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/reference_markers.fasta -out GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:09,376] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:09,380] [INFO] Selected 6 target genomes.
[2023-06-30 20:55:09,380] [INFO] Target genome list was writen to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/target_genomes.txt
[2023-06-30 20:55:09,382] [INFO] Task started: fastANI
[2023-06-30 20:55:09,382] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac50242-e8be-4de8-a49d-a9877f7813c0/GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna.gz --refList GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/target_genomes.txt --output GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:12,615] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:12,615] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:12,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:12,617] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:55:12,618] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:55:12,618] [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 20:55:12,620] [INFO] DFAST Taxonomy check result was written to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/tc_result.tsv
[2023-06-30 20:55:12,621] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:12,621] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:12,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/checkm_data
[2023-06-30 20:55:12,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:12,672] [INFO] Task started: CheckM
[2023-06-30 20:55:12,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/checkm_input GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/checkm_result
[2023-06-30 20:56:02,985] [INFO] Task succeeded: CheckM
[2023-06-30 20:56:02,987] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.19%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:56:03,022] [INFO] ===== Completeness check finished =====
[2023-06-30 20:56:03,023] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:56:03,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/markers.fasta)
[2023-06-30 20:56:03,024] [INFO] Task started: Blastn
[2023-06-30 20:56:03,024] [INFO] Running command: blastn -query GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/markers.fasta -db /var/lib/cwl/stg743d4931-210e-42c2-95a2-087c2ceea83d/dqc_reference/reference_markers_gtdb.fasta -out GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:56:03,499] [INFO] Task succeeded: Blastn
[2023-06-30 20:56:03,504] [INFO] Selected 8 target genomes.
[2023-06-30 20:56:03,504] [INFO] Target genome list was writen to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:56:03,508] [INFO] Task started: fastANI
[2023-06-30 20:56:03,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgeac50242-e8be-4de8-a49d-a9877f7813c0/GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna.gz --refList GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/target_genomes_gtdb.txt --output GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:56:09,517] [INFO] Task succeeded: fastANI
[2023-06-30 20:56:09,528] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:56:09,528] [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_903878265.1	s__UBA4417 sp903878265	99.1562	491	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.16	98.69	0.84	0.83	4	conclusive
GCA_903946925.1	s__UBA4417 sp903946925	83.2238	388	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.75	99.75	0.91	0.91	2	-
GCA_903917425.1	s__UBA4417 sp903917425	78.5253	132	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903913645.1	s__UBA4417 sp903913645	77.6694	84	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879715.1	s__UBA4417 sp903879715	77.5795	101	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.96	99.96	0.96	0.96	2	-
GCA_903822525.1	s__UBA4417 sp903822525	77.3849	103	555	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	98.45	95.43	0.85	0.81	12	-
--------------------------------------------------------------------------------
[2023-06-30 20:56:09,530] [INFO] GTDB search result was written to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/result_gtdb.tsv
[2023-06-30 20:56:09,531] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:56:09,534] [INFO] DFAST_QC result json was written to GCA_903832845.1_freshwater_MAG_---_Day6-2_bin-608_genomic.fna/dqc_result.json
[2023-06-30 20:56:09,534] [INFO] DFAST_QC completed!
[2023-06-30 20:56:09,534] [INFO] Total running time: 0h1m19s