[2023-06-30 04:51:43,381] [INFO] DFAST_QC pipeline started.
[2023-06-30 04:51:43,384] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 04:51:43,384] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference
[2023-06-30 04:51:44,780] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 04:51:44,781] [INFO] Task started: Prodigal
[2023-06-30 04:51:44,782] [INFO] Running command: gunzip -c /var/lib/cwl/stg82688e64-23ae-4690-a95f-dbb0550006e6/GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna.gz | prodigal -d GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/cds.fna -a GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 04:51:47,590] [INFO] Task succeeded: Prodigal
[2023-06-30 04:51:47,591] [INFO] Task started: HMMsearch
[2023-06-30 04:51:47,591] [INFO] Running command: hmmsearch --tblout GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/reference_markers.hmm GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/protein.faa > /dev/null
[2023-06-30 04:51:47,773] [INFO] Task succeeded: HMMsearch
[2023-06-30 04:51:47,775] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg82688e64-23ae-4690-a95f-dbb0550006e6/GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna.gz]
[2023-06-30 04:51:47,794] [INFO] Query marker FASTA was written to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/markers.fasta
[2023-06-30 04:51:47,795] [INFO] Task started: Blastn
[2023-06-30 04:51:47,795] [INFO] Running command: blastn -query GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/reference_markers.fasta -out GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:51:48,307] [INFO] Task succeeded: Blastn
[2023-06-30 04:51:48,312] [INFO] Selected 10 target genomes.
[2023-06-30 04:51:48,312] [INFO] Target genome list was writen to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/target_genomes.txt
[2023-06-30 04:51:48,315] [INFO] Task started: fastANI
[2023-06-30 04:51:48,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg82688e64-23ae-4690-a95f-dbb0550006e6/GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna.gz --refList GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/target_genomes.txt --output GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 04:51:55,035] [INFO] Task succeeded: fastANI
[2023-06-30 04:51:55,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 04:51:55,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 04:51:55,038] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 04:51:55,038] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 04:51:55,038] [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 04:51:55,040] [INFO] DFAST Taxonomy check result was written to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/tc_result.tsv
[2023-06-30 04:51:55,041] [INFO] ===== Taxonomy check completed =====
[2023-06-30 04:51:55,041] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 04:51:55,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/checkm_data
[2023-06-30 04:51:55,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 04:51:55,067] [INFO] Task started: CheckM
[2023-06-30 04:51:55,067] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/checkm_input GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/checkm_result
[2023-06-30 04:52:12,662] [INFO] Task succeeded: CheckM
[2023-06-30 04:52:12,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 04:52:12,683] [INFO] ===== Completeness check finished =====
[2023-06-30 04:52:12,683] [INFO] ===== Start GTDB Search =====
[2023-06-30 04:52:12,683] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/markers.fasta)
[2023-06-30 04:52:12,684] [INFO] Task started: Blastn
[2023-06-30 04:52:12,684] [INFO] Running command: blastn -query GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b850faa-8237-4feb-9bc8-c2a634bccacb/dqc_reference/reference_markers_gtdb.fasta -out GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 04:52:13,194] [INFO] Task succeeded: Blastn
[2023-06-30 04:52:13,199] [INFO] Selected 7 target genomes.
[2023-06-30 04:52:13,200] [INFO] Target genome list was writen to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 04:52:13,205] [INFO] Task started: fastANI
[2023-06-30 04:52:13,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg82688e64-23ae-4690-a95f-dbb0550006e6/GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna.gz --refList GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/target_genomes_gtdb.txt --output GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 04:52:15,846] [INFO] Task succeeded: fastANI
[2023-06-30 04:52:15,857] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 04:52:15,857] [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_903880855.1	s__Limnohabitans sp903880855	98.5391	131	137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	99.14	98.09	0.92	0.91	4	conclusive
GCA_009923345.1	s__Limnohabitans sp009923345	87.1779	115	137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005786815.1	s__Limnohabitans sp005786815	87.0151	91	137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018969975.1	s__Limnohabitans sp018969975	84.4195	101	137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002347905.1	s__Limnohabitans sp002347905	84.3578	101	137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Limnohabitans	95.0	98.39	98.39	0.80	0.80	2	-
--------------------------------------------------------------------------------
[2023-06-30 04:52:15,859] [INFO] GTDB search result was written to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/result_gtdb.tsv
[2023-06-30 04:52:15,860] [INFO] ===== GTDB Search completed =====
[2023-06-30 04:52:15,863] [INFO] DFAST_QC result json was written to GCA_903848245.1_freshwater_MAG_---_Kiruna3_bin-4059_genomic.fna/dqc_result.json
[2023-06-30 04:52:15,863] [INFO] DFAST_QC completed!
[2023-06-30 04:52:15,863] [INFO] Total running time: 0h0m32s