[2023-06-30 08:42:59,813] [INFO] DFAST_QC pipeline started.
[2023-06-30 08:42:59,815] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 08:42:59,815] [INFO] DQC Reference Directory: /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference
[2023-06-30 08:43:01,930] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 08:43:01,931] [INFO] Task started: Prodigal
[2023-06-30 08:43:01,932] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f74fb7a-874a-4cd8-bd25-c1d088873ba2/GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna.gz | prodigal -d GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/cds.fna -a GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 08:43:29,380] [INFO] Task succeeded: Prodigal
[2023-06-30 08:43:29,381] [INFO] Task started: HMMsearch
[2023-06-30 08:43:29,381] [INFO] Running command: hmmsearch --tblout GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/reference_markers.hmm GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/protein.faa > /dev/null
[2023-06-30 08:43:29,788] [INFO] Task succeeded: HMMsearch
[2023-06-30 08:43:29,790] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg6f74fb7a-874a-4cd8-bd25-c1d088873ba2/GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna.gz]
[2023-06-30 08:43:29,837] [INFO] Query marker FASTA was written to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/markers.fasta
[2023-06-30 08:43:29,838] [INFO] Task started: Blastn
[2023-06-30 08:43:29,838] [INFO] Running command: blastn -query GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/markers.fasta -db /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/reference_markers.fasta -out GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:43:33,032] [INFO] Task succeeded: Blastn
[2023-06-30 08:43:33,037] [INFO] Selected 7 target genomes.
[2023-06-30 08:43:33,038] [INFO] Target genome list was writen to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/target_genomes.txt
[2023-06-30 08:43:33,041] [INFO] Task started: fastANI
[2023-06-30 08:43:33,042] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f74fb7a-874a-4cd8-bd25-c1d088873ba2/GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna.gz --refList GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/target_genomes.txt --output GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 08:43:37,230] [INFO] Task succeeded: fastANI
[2023-06-30 08:43:37,231] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 08:43:37,231] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 08:43:37,233] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 08:43:37,233] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 08:43:37,233] [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 08:43:37,235] [INFO] DFAST Taxonomy check result was written to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/tc_result.tsv
[2023-06-30 08:43:37,236] [INFO] ===== Taxonomy check completed =====
[2023-06-30 08:43:37,236] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 08:43:37,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/checkm_data
[2023-06-30 08:43:37,239] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 08:43:37,289] [INFO] Task started: CheckM
[2023-06-30 08:43:37,289] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/checkm_input GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/checkm_result
[2023-06-30 08:44:52,179] [INFO] Task succeeded: CheckM
[2023-06-30 08:44:52,181] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 25.93%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 08:44:52,201] [INFO] ===== Completeness check finished =====
[2023-06-30 08:44:52,202] [INFO] ===== Start GTDB Search =====
[2023-06-30 08:44:52,202] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/markers.fasta)
[2023-06-30 08:44:52,202] [INFO] Task started: Blastn
[2023-06-30 08:44:52,202] [INFO] Running command: blastn -query GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/markers.fasta -db /var/lib/cwl/stga9494eed-0948-4904-9bf5-691db3aa0b80/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 08:44:52,681] [INFO] Task succeeded: Blastn
[2023-06-30 08:44:52,686] [INFO] Selected 8 target genomes.
[2023-06-30 08:44:52,686] [INFO] Target genome list was writen to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 08:44:52,694] [INFO] Task started: fastANI
[2023-06-30 08:44:52,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f74fb7a-874a-4cd8-bd25-c1d088873ba2/GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna.gz --refList GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/target_genomes_gtdb.txt --output GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 08:44:59,232] [INFO] Task succeeded: fastANI
[2023-06-30 08:44:59,244] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 08:44:59,244] [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_903850425.1	s__UBA11358 sp903850425	99.823	582	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903884535.1	s__UBA11358 sp903884535	80.9346	223	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.82	0.93	0.89	5	-
GCA_003455565.1	s__UBA11358 sp003455565	80.2301	166	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903917705.1	s__UBA11358 sp903917705	79.7892	145	605	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	79.5993	264	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903870815.1	s__UBA11358 sp903870815	78.9447	121	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.83	99.83	0.93	0.93	2	-
GCA_003151855.1	s__UBA11358 sp003151855	78.8313	157	605	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 08:44:59,252] [INFO] GTDB search result was written to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/result_gtdb.tsv
[2023-06-30 08:44:59,252] [INFO] ===== GTDB Search completed =====
[2023-06-30 08:44:59,256] [INFO] DFAST_QC result json was written to GCA_903830435.1_freshwater_MAG_---_MJ120827A_bin-590_genomic.fna/dqc_result.json
[2023-06-30 08:44:59,256] [INFO] DFAST_QC completed!
[2023-06-30 08:44:59,256] [INFO] Total running time: 0h1m59s