[2023-06-28 17:03:06,444] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:03:06,446] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:03:06,447] [INFO] DQC Reference Directory: /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference
[2023-06-28 17:03:07,711] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:03:07,712] [INFO] Task started: Prodigal
[2023-06-28 17:03:07,713] [INFO] Running command: gunzip -c /var/lib/cwl/stg5df3cf03-6da7-4746-a97e-2af31abb95bb/GCA_944324245.1_E09_bin203_genomic.fna.gz | prodigal -d GCA_944324245.1_E09_bin203_genomic.fna/cds.fna -a GCA_944324245.1_E09_bin203_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:03:11,426] [INFO] Task succeeded: Prodigal
[2023-06-28 17:03:11,427] [INFO] Task started: HMMsearch
[2023-06-28 17:03:11,427] [INFO] Running command: hmmsearch --tblout GCA_944324245.1_E09_bin203_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/reference_markers.hmm GCA_944324245.1_E09_bin203_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:03:11,695] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:03:11,697] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5df3cf03-6da7-4746-a97e-2af31abb95bb/GCA_944324245.1_E09_bin203_genomic.fna.gz]
[2023-06-28 17:03:11,721] [INFO] Query marker FASTA was written to GCA_944324245.1_E09_bin203_genomic.fna/markers.fasta
[2023-06-28 17:03:11,722] [INFO] Task started: Blastn
[2023-06-28 17:03:11,722] [INFO] Running command: blastn -query GCA_944324245.1_E09_bin203_genomic.fna/markers.fasta -db /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/reference_markers.fasta -out GCA_944324245.1_E09_bin203_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:03:12,299] [INFO] Task succeeded: Blastn
[2023-06-28 17:03:12,303] [INFO] Selected 15 target genomes.
[2023-06-28 17:03:12,303] [INFO] Target genome list was writen to GCA_944324245.1_E09_bin203_genomic.fna/target_genomes.txt
[2023-06-28 17:03:12,306] [INFO] Task started: fastANI
[2023-06-28 17:03:12,306] [INFO] Running command: fastANI --query /var/lib/cwl/stg5df3cf03-6da7-4746-a97e-2af31abb95bb/GCA_944324245.1_E09_bin203_genomic.fna.gz --refList GCA_944324245.1_E09_bin203_genomic.fna/target_genomes.txt --output GCA_944324245.1_E09_bin203_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:03:20,412] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:20,413] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:03:20,413] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:03:20,415] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:03:20,416] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 17:03:20,416] [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
--------------------------------------------------------------------------------
[2023-06-28 17:03:20,418] [INFO] DFAST Taxonomy check result was written to GCA_944324245.1_E09_bin203_genomic.fna/tc_result.tsv
[2023-06-28 17:03:20,419] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:03:20,419] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:03:20,420] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/checkm_data
[2023-06-28 17:03:20,425] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:03:20,448] [INFO] Task started: CheckM
[2023-06-28 17:03:20,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324245.1_E09_bin203_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324245.1_E09_bin203_genomic.fna/checkm_input GCA_944324245.1_E09_bin203_genomic.fna/checkm_result
[2023-06-28 17:03:39,656] [INFO] Task succeeded: CheckM
[2023-06-28 17:03:39,658] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.61%
Contamintation: 2.08%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 17:03:39,680] [INFO] ===== Completeness check finished =====
[2023-06-28 17:03:39,680] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:03:39,681] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324245.1_E09_bin203_genomic.fna/markers.fasta)
[2023-06-28 17:03:39,681] [INFO] Task started: Blastn
[2023-06-28 17:03:39,681] [INFO] Running command: blastn -query GCA_944324245.1_E09_bin203_genomic.fna/markers.fasta -db /var/lib/cwl/stged0b696a-d24e-4e21-bc7d-ef2421bd8e77/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324245.1_E09_bin203_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:03:40,474] [INFO] Task succeeded: Blastn
[2023-06-28 17:03:40,478] [INFO] Selected 18 target genomes.
[2023-06-28 17:03:40,478] [INFO] Target genome list was writen to GCA_944324245.1_E09_bin203_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:03:40,484] [INFO] Task started: fastANI
[2023-06-28 17:03:40,485] [INFO] Running command: fastANI --query /var/lib/cwl/stg5df3cf03-6da7-4746-a97e-2af31abb95bb/GCA_944324245.1_E09_bin203_genomic.fna.gz --refList GCA_944324245.1_E09_bin203_genomic.fna/target_genomes_gtdb.txt --output GCA_944324245.1_E09_bin203_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:03:46,290] [INFO] Task succeeded: fastANI
[2023-06-28 17:03:46,303] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:03:46,303] [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_000980375.1	s__Limenecus avicola	78.5613	268	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	98.45	97.78	0.95	0.92	8	-
GCA_018362895.1	s__Limenecus sp018362895	77.8823	222	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Limenecus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900547155.1	s__Spyradomonas excrementavium	77.0218	98	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.06	98.43	0.95	0.94	4	-
GCA_900547585.1	s__Spyradomonas sp900547585	76.7205	76	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Spyradomonas	95.0	99.89	99.89	0.88	0.88	2	-
GCA_900551675.1	s__Stercorousia sp900551675	76.6099	53	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	100.00	100.00	0.98	0.98	2	-
GCA_910588555.1	s__Stercorousia sp910588555	76.4207	54	617	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__Stercorousia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:03:46,305] [INFO] GTDB search result was written to GCA_944324245.1_E09_bin203_genomic.fna/result_gtdb.tsv
[2023-06-28 17:03:46,306] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:03:46,308] [INFO] DFAST_QC result json was written to GCA_944324245.1_E09_bin203_genomic.fna/dqc_result.json
[2023-06-28 17:03:46,309] [INFO] DFAST_QC completed!
[2023-06-28 17:03:46,309] [INFO] Total running time: 0h0m40s