[2023-06-28 03:13:01,269] [INFO] DFAST_QC pipeline started.
[2023-06-28 03:13:01,274] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 03:13:01,274] [INFO] DQC Reference Directory: /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference
[2023-06-28 03:13:03,563] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 03:13:03,564] [INFO] Task started: Prodigal
[2023-06-28 03:13:03,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg6b846cd4-0748-49f0-9c05-17c718fe494f/GCA_944373145.1_BRZ_FM_bin62_genomic.fna.gz | prodigal -d GCA_944373145.1_BRZ_FM_bin62_genomic.fna/cds.fna -a GCA_944373145.1_BRZ_FM_bin62_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 03:13:05,650] [INFO] Task succeeded: Prodigal
[2023-06-28 03:13:05,651] [INFO] Task started: HMMsearch
[2023-06-28 03:13:05,651] [INFO] Running command: hmmsearch --tblout GCA_944373145.1_BRZ_FM_bin62_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/reference_markers.hmm GCA_944373145.1_BRZ_FM_bin62_genomic.fna/protein.faa > /dev/null
[2023-06-28 03:13:05,865] [INFO] Task succeeded: HMMsearch
[2023-06-28 03:13:05,867] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6b846cd4-0748-49f0-9c05-17c718fe494f/GCA_944373145.1_BRZ_FM_bin62_genomic.fna.gz]
[2023-06-28 03:13:05,888] [INFO] Query marker FASTA was written to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/markers.fasta
[2023-06-28 03:13:05,888] [INFO] Task started: Blastn
[2023-06-28 03:13:05,888] [INFO] Running command: blastn -query GCA_944373145.1_BRZ_FM_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/reference_markers.fasta -out GCA_944373145.1_BRZ_FM_bin62_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:13:08,440] [INFO] Task succeeded: Blastn
[2023-06-28 03:13:08,446] [INFO] Selected 30 target genomes.
[2023-06-28 03:13:08,446] [INFO] Target genome list was writen to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/target_genomes.txt
[2023-06-28 03:13:08,467] [INFO] Task started: fastANI
[2023-06-28 03:13:08,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b846cd4-0748-49f0-9c05-17c718fe494f/GCA_944373145.1_BRZ_FM_bin62_genomic.fna.gz --refList GCA_944373145.1_BRZ_FM_bin62_genomic.fna/target_genomes.txt --output GCA_944373145.1_BRZ_FM_bin62_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 03:13:19,180] [INFO] Task succeeded: fastANI
[2023-06-28 03:13:19,181] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 03:13:19,182] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 03:13:19,184] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 03:13:19,184] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 03:13:19,184] [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 03:13:19,187] [INFO] DFAST Taxonomy check result was written to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/tc_result.tsv
[2023-06-28 03:13:19,188] [INFO] ===== Taxonomy check completed =====
[2023-06-28 03:13:19,188] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 03:13:19,188] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/checkm_data
[2023-06-28 03:13:19,193] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 03:13:19,223] [INFO] Task started: CheckM
[2023-06-28 03:13:19,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944373145.1_BRZ_FM_bin62_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944373145.1_BRZ_FM_bin62_genomic.fna/checkm_input GCA_944373145.1_BRZ_FM_bin62_genomic.fna/checkm_result
[2023-06-28 03:13:33,569] [INFO] Task succeeded: CheckM
[2023-06-28 03:13:33,571] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 03:13:33,593] [INFO] ===== Completeness check finished =====
[2023-06-28 03:13:33,594] [INFO] ===== Start GTDB Search =====
[2023-06-28 03:13:33,594] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944373145.1_BRZ_FM_bin62_genomic.fna/markers.fasta)
[2023-06-28 03:13:33,594] [INFO] Task started: Blastn
[2023-06-28 03:13:33,595] [INFO] Running command: blastn -query GCA_944373145.1_BRZ_FM_bin62_genomic.fna/markers.fasta -db /var/lib/cwl/stge7822832-cee0-4c5e-88a3-1bbafa553dee/dqc_reference/reference_markers_gtdb.fasta -out GCA_944373145.1_BRZ_FM_bin62_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 03:13:34,395] [INFO] Task succeeded: Blastn
[2023-06-28 03:13:34,402] [INFO] Selected 21 target genomes.
[2023-06-28 03:13:34,402] [INFO] Target genome list was writen to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 03:13:34,415] [INFO] Task started: fastANI
[2023-06-28 03:13:34,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg6b846cd4-0748-49f0-9c05-17c718fe494f/GCA_944373145.1_BRZ_FM_bin62_genomic.fna.gz --refList GCA_944373145.1_BRZ_FM_bin62_genomic.fna/target_genomes_gtdb.txt --output GCA_944373145.1_BRZ_FM_bin62_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 03:13:39,221] [INFO] Task succeeded: fastANI
[2023-06-28 03:13:39,245] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 03:13:39,245] [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_002425325.1	s__UBA5578 sp002425325	78.2201	104	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910584165.1	s__UBA5578 sp910584165	77.9848	135	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589375.1	s__UBA5578 sp910589375	77.7207	127	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017527675.1	s__RGIG6635 sp017527675	77.5505	78	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RGIG6635	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017462455.1	s__UMGS1613 sp017462455	77.4558	67	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059285.1	s__SIG208 sp015059285	77.1459	66	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__SIG208	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410525.1	s__UMGS1613 sp017410525	77.0221	77	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017536505.1	s__UMGS1613 sp017536505	77.0007	67	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773675.1	s__RUG11890 sp902773675	76.6943	60	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11890	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795975.1	s__UBA5578 sp902795975	76.5895	85	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059155.1	s__UMGS1613 sp015059155	76.4604	66	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012520435.1	s__JAAYOI01 sp012520435	76.3939	64	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__JAAYOI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017436345.1	s__RUG11788 sp017436345	76.2353	52	420	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG11788	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 03:13:39,247] [INFO] GTDB search result was written to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/result_gtdb.tsv
[2023-06-28 03:13:39,248] [INFO] ===== GTDB Search completed =====
[2023-06-28 03:13:39,251] [INFO] DFAST_QC result json was written to GCA_944373145.1_BRZ_FM_bin62_genomic.fna/dqc_result.json
[2023-06-28 03:13:39,251] [INFO] DFAST_QC completed!
[2023-06-28 03:13:39,251] [INFO] Total running time: 0h0m38s