[2023-06-30 18:53:00,482] [INFO] DFAST_QC pipeline started.
[2023-06-30 18:53:00,484] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 18:53:00,484] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference
[2023-06-30 18:53:02,991] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 18:53:02,992] [INFO] Task started: Prodigal
[2023-06-30 18:53:02,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg2c223bfd-3f8a-40cf-b1c4-9ebd744b32db/GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna.gz | prodigal -d GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/cds.fna -a GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 18:53:05,545] [INFO] Task succeeded: Prodigal
[2023-06-30 18:53:05,545] [INFO] Task started: HMMsearch
[2023-06-30 18:53:05,545] [INFO] Running command: hmmsearch --tblout GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/reference_markers.hmm GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/protein.faa > /dev/null
[2023-06-30 18:53:05,745] [INFO] Task succeeded: HMMsearch
[2023-06-30 18:53:05,746] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2c223bfd-3f8a-40cf-b1c4-9ebd744b32db/GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna.gz]
[2023-06-30 18:53:05,771] [INFO] Query marker FASTA was written to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/markers.fasta
[2023-06-30 18:53:05,771] [INFO] Task started: Blastn
[2023-06-30 18:53:05,771] [INFO] Running command: blastn -query GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/reference_markers.fasta -out GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:53:07,347] [INFO] Task succeeded: Blastn
[2023-06-30 18:53:07,351] [INFO] Selected 10 target genomes.
[2023-06-30 18:53:07,352] [INFO] Target genome list was writen to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/target_genomes.txt
[2023-06-30 18:53:07,355] [INFO] Task started: fastANI
[2023-06-30 18:53:07,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c223bfd-3f8a-40cf-b1c4-9ebd744b32db/GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna.gz --refList GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/target_genomes.txt --output GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 18:53:12,661] [INFO] Task succeeded: fastANI
[2023-06-30 18:53:12,662] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 18:53:12,662] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 18:53:12,664] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 18:53:12,664] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 18:53:12,665] [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 18:53:12,667] [INFO] DFAST Taxonomy check result was written to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/tc_result.tsv
[2023-06-30 18:53:12,668] [INFO] ===== Taxonomy check completed =====
[2023-06-30 18:53:12,668] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 18:53:12,669] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/checkm_data
[2023-06-30 18:53:12,672] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 18:53:12,689] [INFO] Task started: CheckM
[2023-06-30 18:53:12,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/checkm_input GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/checkm_result
[2023-06-30 18:53:29,484] [INFO] Task succeeded: CheckM
[2023-06-30 18:53:29,485] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 18:53:29,507] [INFO] ===== Completeness check finished =====
[2023-06-30 18:53:29,507] [INFO] ===== Start GTDB Search =====
[2023-06-30 18:53:29,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/markers.fasta)
[2023-06-30 18:53:29,508] [INFO] Task started: Blastn
[2023-06-30 18:53:29,508] [INFO] Running command: blastn -query GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4a64067-90d6-4722-bba3-b93e94cd24eb/dqc_reference/reference_markers_gtdb.fasta -out GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 18:53:30,239] [INFO] Task succeeded: Blastn
[2023-06-30 18:53:30,243] [INFO] Selected 10 target genomes.
[2023-06-30 18:53:30,244] [INFO] Target genome list was writen to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 18:53:30,245] [INFO] Task started: fastANI
[2023-06-30 18:53:30,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg2c223bfd-3f8a-40cf-b1c4-9ebd744b32db/GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna.gz --refList GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/target_genomes_gtdb.txt --output GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 18:53:32,277] [INFO] Task succeeded: fastANI
[2023-06-30 18:53:32,295] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 18:53:32,296] [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_903867285.1	s__PALSA-747 sp903867285	98.1568	172	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.56	98.05	0.76	0.69	12	conclusive
GCA_903827345.1	s__PALSA-747 sp903827345	87.9677	158	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	97.69	97.69	0.77	0.77	2	-
GCA_903933585.1	s__PALSA-747 sp903933585	85.473	190	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.42	99.37	0.91	0.88	4	-
GCA_903899375.1	s__PALSA-747 sp903899375	83.6375	167	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.46	99.00	0.86	0.79	59	-
GCA_903891755.1	s__PALSA-747 sp903891755	79.2551	79	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.94	98.90	0.76	0.73	3	-
GCA_903932705.1	s__PALSA-747 sp903932705	78.4676	69	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839355.1	s__PALSA-747 sp903839355	78.2405	50	236	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 18:53:32,298] [INFO] GTDB search result was written to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/result_gtdb.tsv
[2023-06-30 18:53:32,299] [INFO] ===== GTDB Search completed =====
[2023-06-30 18:53:32,303] [INFO] DFAST_QC result json was written to GCA_903852425.1_freshwater_MAG_---_MJ130617B_bin-676_genomic.fna/dqc_result.json
[2023-06-30 18:53:32,303] [INFO] DFAST_QC completed!
[2023-06-30 18:53:32,303] [INFO] Total running time: 0h0m32s