[2023-07-01 04:39:49,097] [INFO] DFAST_QC pipeline started.
[2023-07-01 04:39:49,105] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 04:39:49,105] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference
[2023-07-01 04:39:50,485] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 04:39:50,486] [INFO] Task started: Prodigal
[2023-07-01 04:39:50,486] [INFO] Running command: gunzip -c /var/lib/cwl/stgd03ed333-ac8f-487b-a7e0-d7c07b61d106/GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna.gz | prodigal -d GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/cds.fna -a GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 04:40:02,242] [INFO] Task succeeded: Prodigal
[2023-07-01 04:40:02,242] [INFO] Task started: HMMsearch
[2023-07-01 04:40:02,243] [INFO] Running command: hmmsearch --tblout GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/reference_markers.hmm GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/protein.faa > /dev/null
[2023-07-01 04:40:02,416] [INFO] Task succeeded: HMMsearch
[2023-07-01 04:40:02,418] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgd03ed333-ac8f-487b-a7e0-d7c07b61d106/GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna.gz]
[2023-07-01 04:40:02,441] [INFO] Query marker FASTA was written to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/markers.fasta
[2023-07-01 04:40:02,442] [INFO] Task started: Blastn
[2023-07-01 04:40:02,442] [INFO] Running command: blastn -query GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/reference_markers.fasta -out GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:40:02,949] [INFO] Task succeeded: Blastn
[2023-07-01 04:40:02,952] [INFO] Selected 5 target genomes.
[2023-07-01 04:40:02,953] [INFO] Target genome list was writen to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/target_genomes.txt
[2023-07-01 04:40:02,954] [INFO] Task started: fastANI
[2023-07-01 04:40:02,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgd03ed333-ac8f-487b-a7e0-d7c07b61d106/GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna.gz --refList GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/target_genomes.txt --output GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 04:40:05,853] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:05,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 04:40:05,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 04:40:05,855] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 04:40:05,855] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 04:40:05,855] [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 04:40:05,857] [INFO] DFAST Taxonomy check result was written to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/tc_result.tsv
[2023-07-01 04:40:05,858] [INFO] ===== Taxonomy check completed =====
[2023-07-01 04:40:05,858] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 04:40:05,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/checkm_data
[2023-07-01 04:40:05,862] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 04:40:05,886] [INFO] Task started: CheckM
[2023-07-01 04:40:05,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/checkm_input GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/checkm_result
[2023-07-01 04:40:42,955] [INFO] Task succeeded: CheckM
[2023-07-01 04:40:42,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 52.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 04:40:42,977] [INFO] ===== Completeness check finished =====
[2023-07-01 04:40:42,977] [INFO] ===== Start GTDB Search =====
[2023-07-01 04:40:42,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/markers.fasta)
[2023-07-01 04:40:42,978] [INFO] Task started: Blastn
[2023-07-01 04:40:42,978] [INFO] Running command: blastn -query GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7f5da1b-2a8e-4726-882a-85963752d432/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 04:40:43,500] [INFO] Task succeeded: Blastn
[2023-07-01 04:40:43,504] [INFO] Selected 8 target genomes.
[2023-07-01 04:40:43,505] [INFO] Target genome list was writen to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 04:40:43,506] [INFO] Task started: fastANI
[2023-07-01 04:40:43,506] [INFO] Running command: fastANI --query /var/lib/cwl/stgd03ed333-ac8f-487b-a7e0-d7c07b61d106/GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna.gz --refList GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/target_genomes_gtdb.txt --output GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 04:40:48,235] [INFO] Task succeeded: fastANI
[2023-07-01 04:40:48,243] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 04:40:48,243] [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_903878805.1	s__UBA11358 sp903878805	99.5392	348	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.90	0.92	0.92	2	conclusive
GCA_903833055.1	s__UBA11358 sp903833055	82.8737	262	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.65	99.64	0.85	0.82	3	-
GCA_003139955.1	s__UBA11358 sp003139955	81.9531	240	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.56	99.56	0.93	0.93	2	-
GCA_903861445.1	s__UBA11358 sp903861445	79.637	185	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903889895.1	s__UBA11358 sp903889895	79.5367	176	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903921455.1	s__UBA11358 sp903921455	79.2555	229	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944085.1	s__UBA11358 sp903944085	79.2116	235	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903827955.1	s__UBA11358 sp903827955	79.1513	195	401	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.89	99.82	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2023-07-01 04:40:48,245] [INFO] GTDB search result was written to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/result_gtdb.tsv
[2023-07-01 04:40:48,245] [INFO] ===== GTDB Search completed =====
[2023-07-01 04:40:48,248] [INFO] DFAST_QC result json was written to GCA_903866545.1_freshwater_MAG_---_AlinenLipids_bin-2669_genomic.fna/dqc_result.json
[2023-07-01 04:40:48,248] [INFO] DFAST_QC completed!
[2023-07-01 04:40:48,248] [INFO] Total running time: 0h0m59s