[2023-06-05 18:50:13,480] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:50:13,482] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:50:13,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference
[2023-06-05 18:50:14,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:50:14,583] [INFO] Task started: Prodigal
[2023-06-05 18:50:14,583] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f51916b-a7bd-47d6-9852-3810179e8416/GCA_934718005.1_ERR7745743_bin.124_genomic.fna.gz | prodigal -d GCA_934718005.1_ERR7745743_bin.124_genomic.fna/cds.fna -a GCA_934718005.1_ERR7745743_bin.124_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:50:18,173] [INFO] Task succeeded: Prodigal
[2023-06-05 18:50:18,173] [INFO] Task started: HMMsearch
[2023-06-05 18:50:18,173] [INFO] Running command: hmmsearch --tblout GCA_934718005.1_ERR7745743_bin.124_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/reference_markers.hmm GCA_934718005.1_ERR7745743_bin.124_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:50:18,350] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:50:18,351] [INFO] Found 6/6 markers.
[2023-06-05 18:50:18,370] [INFO] Query marker FASTA was written to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/markers.fasta
[2023-06-05 18:50:18,370] [INFO] Task started: Blastn
[2023-06-05 18:50:18,371] [INFO] Running command: blastn -query GCA_934718005.1_ERR7745743_bin.124_genomic.fna/markers.fasta -db /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/reference_markers.fasta -out GCA_934718005.1_ERR7745743_bin.124_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:50:18,904] [INFO] Task succeeded: Blastn
[2023-06-05 18:50:18,911] [INFO] Selected 27 target genomes.
[2023-06-05 18:50:18,911] [INFO] Target genome list was writen to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/target_genomes.txt
[2023-06-05 18:50:18,924] [INFO] Task started: fastANI
[2023-06-05 18:50:18,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f51916b-a7bd-47d6-9852-3810179e8416/GCA_934718005.1_ERR7745743_bin.124_genomic.fna.gz --refList GCA_934718005.1_ERR7745743_bin.124_genomic.fna/target_genomes.txt --output GCA_934718005.1_ERR7745743_bin.124_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:50:34,522] [INFO] Task succeeded: fastANI
[2023-06-05 18:50:34,522] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:50:34,525] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:50:34,526] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:50:34,526] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:50:34,526] [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
--------------------------------------------------------------------------------
[2023-06-05 18:50:34,528] [INFO] DFAST Taxonomy check result was written to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/tc_result.tsv
[2023-06-05 18:50:34,528] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:50:34,528] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:50:34,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/checkm_data
[2023-06-05 18:50:34,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:50:34,556] [INFO] Task started: CheckM
[2023-06-05 18:50:34,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934718005.1_ERR7745743_bin.124_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934718005.1_ERR7745743_bin.124_genomic.fna/checkm_input GCA_934718005.1_ERR7745743_bin.124_genomic.fna/checkm_result
[2023-06-05 18:50:52,834] [INFO] Task succeeded: CheckM
[2023-06-05 18:50:52,835] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:50:52,854] [INFO] ===== Completeness check finished =====
[2023-06-05 18:50:52,854] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:50:52,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934718005.1_ERR7745743_bin.124_genomic.fna/markers.fasta)
[2023-06-05 18:50:52,855] [INFO] Task started: Blastn
[2023-06-05 18:50:52,855] [INFO] Running command: blastn -query GCA_934718005.1_ERR7745743_bin.124_genomic.fna/markers.fasta -db /var/lib/cwl/stg227fa898-a78b-445b-9ebb-f03bb485ea46/dqc_reference/reference_markers_gtdb.fasta -out GCA_934718005.1_ERR7745743_bin.124_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:50:53,680] [INFO] Task succeeded: Blastn
[2023-06-05 18:50:53,684] [INFO] Selected 17 target genomes.
[2023-06-05 18:50:53,684] [INFO] Target genome list was writen to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:50:53,691] [INFO] Task started: fastANI
[2023-06-05 18:50:53,691] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f51916b-a7bd-47d6-9852-3810179e8416/GCA_934718005.1_ERR7745743_bin.124_genomic.fna.gz --refList GCA_934718005.1_ERR7745743_bin.124_genomic.fna/target_genomes_gtdb.txt --output GCA_934718005.1_ERR7745743_bin.124_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:51:00,815] [INFO] Task succeeded: fastANI
[2023-06-05 18:51:00,828] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:51:00,828] [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_900321895.1	s__Scatousia sp900321895	97.3355	375	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	98.96	98.54	0.97	0.93	4	conclusive
GCA_900767135.1	s__Stercorousia sp900767135	80.0688	165	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769645.1	s__Stercorousia sp900769645	78.246	170	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017694215.1	s__Scatousia excrementipullorum	78.147	232	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554385.1	s__Scatousia sp900554385	78.0645	173	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.41	98.83	0.97	0.96	3	-
GCA_018711035.1	s__Scatousia excrementigallinarum	78.0009	183	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Scatousia	95.0	99.20	99.20	0.79	0.79	2	-
GCA_001765415.1	s__Stercorousia sp001765415	77.924	166	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.74	98.70	0.94	0.93	5	-
GCA_900556295.1	s__Stercorousia sp900556295	77.8848	104	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	97.71	97.55	0.83	0.77	3	-
GCA_002405805.1	s__Zag111 sp002405805	77.8049	123	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Zag111	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905216055.1	s__Stercorousia sp905216055	77.7227	162	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588555.1	s__Stercorousia sp910588555	77.7216	157	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769355.1	s__Stercorousia sp900769355	77.6552	173	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770525.1	s__UBA1221 sp900770525	77.6004	163	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA1221	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900548405.1	s__Stercorousia sp001917115	77.5489	161	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	98.35	95.50	0.91	0.85	8	-
GCA_000433095.1	s__Stercorousia sp000433095	77.4003	129	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.53	99.13	0.95	0.93	3	-
GCA_900752845.1	s__Stercorousia sp900752845	77.2155	111	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	99.76	99.76	0.83	0.83	2	-
GCA_017633675.1	s__Stercorousia sp017633675	77.0219	135	583	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:51:00,830] [INFO] GTDB search result was written to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/result_gtdb.tsv
[2023-06-05 18:51:00,831] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:51:00,835] [INFO] DFAST_QC result json was written to GCA_934718005.1_ERR7745743_bin.124_genomic.fna/dqc_result.json
[2023-06-05 18:51:00,835] [INFO] DFAST_QC completed!
[2023-06-05 18:51:00,835] [INFO] Total running time: 0h0m47s