[2023-06-13 15:44:52,118] [INFO] DFAST_QC pipeline started.
[2023-06-13 15:44:52,121] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 15:44:52,121] [INFO] DQC Reference Directory: /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference
[2023-06-13 15:44:53,341] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 15:44:53,342] [INFO] Task started: Prodigal
[2023-06-13 15:44:53,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg706f73a0-f7d8-476e-91aa-9d8fc3eeb99e/GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna.gz | prodigal -d GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/cds.fna -a GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 15:45:03,070] [INFO] Task succeeded: Prodigal
[2023-06-13 15:45:03,070] [INFO] Task started: HMMsearch
[2023-06-13 15:45:03,070] [INFO] Running command: hmmsearch --tblout GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/reference_markers.hmm GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 15:45:03,292] [INFO] Task succeeded: HMMsearch
[2023-06-13 15:45:03,294] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg706f73a0-f7d8-476e-91aa-9d8fc3eeb99e/GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna.gz]
[2023-06-13 15:45:03,321] [INFO] Query marker FASTA was written to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/markers.fasta
[2023-06-13 15:45:03,321] [INFO] Task started: Blastn
[2023-06-13 15:45:03,321] [INFO] Running command: blastn -query GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/reference_markers.fasta -out GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:03,956] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:03,960] [INFO] Selected 20 target genomes.
[2023-06-13 15:45:03,961] [INFO] Target genome list was writen to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/target_genomes.txt
[2023-06-13 15:45:03,975] [INFO] Task started: fastANI
[2023-06-13 15:45:03,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg706f73a0-f7d8-476e-91aa-9d8fc3eeb99e/GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna.gz --refList GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/target_genomes.txt --output GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 15:45:18,151] [INFO] Task succeeded: fastANI
[2023-06-13 15:45:18,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 15:45:18,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 15:45:18,160] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 15:45:18,160] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 15:45:18,161] [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
--------------------------------------------------------------------------------
[2023-06-13 15:45:18,163] [INFO] DFAST Taxonomy check result was written to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/tc_result.tsv
[2023-06-13 15:45:18,164] [INFO] ===== Taxonomy check completed =====
[2023-06-13 15:45:18,164] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 15:45:18,164] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/checkm_data
[2023-06-13 15:45:18,167] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 15:45:18,201] [INFO] Task started: CheckM
[2023-06-13 15:45:18,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/checkm_input GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/checkm_result
[2023-06-13 15:45:49,545] [INFO] Task succeeded: CheckM
[2023-06-13 15:45:49,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 15:45:49,592] [INFO] ===== Completeness check finished =====
[2023-06-13 15:45:49,592] [INFO] ===== Start GTDB Search =====
[2023-06-13 15:45:49,593] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/markers.fasta)
[2023-06-13 15:45:49,593] [INFO] Task started: Blastn
[2023-06-13 15:45:49,593] [INFO] Running command: blastn -query GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47e87a95-b7eb-4785-9b74-bf701a95dd51/dqc_reference/reference_markers_gtdb.fasta -out GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 15:45:50,413] [INFO] Task succeeded: Blastn
[2023-06-13 15:45:50,417] [INFO] Selected 33 target genomes.
[2023-06-13 15:45:50,418] [INFO] Target genome list was writen to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 15:45:50,444] [INFO] Task started: fastANI
[2023-06-13 15:45:50,444] [INFO] Running command: fastANI --query /var/lib/cwl/stg706f73a0-f7d8-476e-91aa-9d8fc3eeb99e/GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna.gz --refList GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 15:46:12,642] [INFO] Task succeeded: fastANI
[2023-06-13 15:46:12,646] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 15:46:12,646] [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_016717205.1	s__OLB15 sp016717205	75.4557	78	986	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB15	95.0	97.47	97.38	0.90	0.87	3	-
GCA_016716525.1	s__OLB13 sp016716525	75.3536	55	986	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__OLB13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788625.1	s__CFX2 sp016788625	75.2344	61	986	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014338005.1	s__CFX2 sp014338005	75.2328	61	986	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Aggregatilineales;f__A4b;g__CFX2	95.0	98.19	98.19	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-13 15:46:12,648] [INFO] GTDB search result was written to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/result_gtdb.tsv
[2023-06-13 15:46:12,649] [INFO] ===== GTDB Search completed =====
[2023-06-13 15:46:12,651] [INFO] DFAST_QC result json was written to GCA_938022205.1_R1_Bin_MAXBIN_116_1_genomic.fna/dqc_result.json
[2023-06-13 15:46:12,651] [INFO] DFAST_QC completed!
[2023-06-13 15:46:12,651] [INFO] Total running time: 0h1m21s