[2023-07-01 05:37:33,448] [INFO] DFAST_QC pipeline started.
[2023-07-01 05:37:33,451] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 05:37:33,451] [INFO] DQC Reference Directory: /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference
[2023-07-01 05:37:34,930] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 05:37:34,931] [INFO] Task started: Prodigal
[2023-07-01 05:37:34,931] [INFO] Running command: gunzip -c /var/lib/cwl/stgd6270ac8-f51b-40f8-a7ea-47d0c4117194/GCA_024408335.1_ASM2440833v1_genomic.fna.gz | prodigal -d GCA_024408335.1_ASM2440833v1_genomic.fna/cds.fna -a GCA_024408335.1_ASM2440833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 05:37:38,183] [INFO] Task succeeded: Prodigal
[2023-07-01 05:37:38,184] [INFO] Task started: HMMsearch
[2023-07-01 05:37:38,184] [INFO] Running command: hmmsearch --tblout GCA_024408335.1_ASM2440833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/reference_markers.hmm GCA_024408335.1_ASM2440833v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 05:37:38,429] [INFO] Task succeeded: HMMsearch
[2023-07-01 05:37:38,430] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd6270ac8-f51b-40f8-a7ea-47d0c4117194/GCA_024408335.1_ASM2440833v1_genomic.fna.gz]
[2023-07-01 05:37:38,449] [INFO] Query marker FASTA was written to GCA_024408335.1_ASM2440833v1_genomic.fna/markers.fasta
[2023-07-01 05:37:38,449] [INFO] Task started: Blastn
[2023-07-01 05:37:38,449] [INFO] Running command: blastn -query GCA_024408335.1_ASM2440833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/reference_markers.fasta -out GCA_024408335.1_ASM2440833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:37:39,006] [INFO] Task succeeded: Blastn
[2023-07-01 05:37:39,010] [INFO] Selected 19 target genomes.
[2023-07-01 05:37:39,011] [INFO] Target genome list was writen to GCA_024408335.1_ASM2440833v1_genomic.fna/target_genomes.txt
[2023-07-01 05:37:39,016] [INFO] Task started: fastANI
[2023-07-01 05:37:39,017] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6270ac8-f51b-40f8-a7ea-47d0c4117194/GCA_024408335.1_ASM2440833v1_genomic.fna.gz --refList GCA_024408335.1_ASM2440833v1_genomic.fna/target_genomes.txt --output GCA_024408335.1_ASM2440833v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 05:37:46,103] [INFO] Task succeeded: fastANI
[2023-07-01 05:37:46,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 05:37:46,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 05:37:46,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 05:37:46,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 05:37:46,106] [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
--------------------------------------------------------------------------------
[2023-07-01 05:37:46,109] [INFO] DFAST Taxonomy check result was written to GCA_024408335.1_ASM2440833v1_genomic.fna/tc_result.tsv
[2023-07-01 05:37:46,109] [INFO] ===== Taxonomy check completed =====
[2023-07-01 05:37:46,110] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 05:37:46,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/checkm_data
[2023-07-01 05:37:46,115] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 05:37:46,132] [INFO] Task started: CheckM
[2023-07-01 05:37:46,132] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024408335.1_ASM2440833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024408335.1_ASM2440833v1_genomic.fna/checkm_input GCA_024408335.1_ASM2440833v1_genomic.fna/checkm_result
[2023-07-01 05:38:03,558] [INFO] Task succeeded: CheckM
[2023-07-01 05:38:03,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 05:38:03,581] [INFO] ===== Completeness check finished =====
[2023-07-01 05:38:03,581] [INFO] ===== Start GTDB Search =====
[2023-07-01 05:38:03,582] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024408335.1_ASM2440833v1_genomic.fna/markers.fasta)
[2023-07-01 05:38:03,582] [INFO] Task started: Blastn
[2023-07-01 05:38:03,582] [INFO] Running command: blastn -query GCA_024408335.1_ASM2440833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga6157608-39a2-4b5e-ae98-d5d1166e1e49/dqc_reference/reference_markers_gtdb.fasta -out GCA_024408335.1_ASM2440833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 05:38:04,370] [INFO] Task succeeded: Blastn
[2023-07-01 05:38:04,375] [INFO] Selected 19 target genomes.
[2023-07-01 05:38:04,376] [INFO] Target genome list was writen to GCA_024408335.1_ASM2440833v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 05:38:04,409] [INFO] Task started: fastANI
[2023-07-01 05:38:04,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgd6270ac8-f51b-40f8-a7ea-47d0c4117194/GCA_024408335.1_ASM2440833v1_genomic.fna.gz --refList GCA_024408335.1_ASM2440833v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024408335.1_ASM2440833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 05:38:11,123] [INFO] Task succeeded: fastANI
[2023-07-01 05:38:11,138] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-07-01 05:38:11,139] [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_902800255.1	s__UBA4951 sp902800255	78.9772	79	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017531065.1	s__UBA4951 sp017531065	78.7219	71	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802355.1	s__UBA4951 sp902802355	78.7003	111	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	96.39	95.33	0.87	0.83	5	-
GCA_017540455.1	s__UBA4951 sp017540455	78.6671	107	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902793515.1	s__UBA4951 sp902793515	78.6044	93	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017618495.1	s__UBA4951 sp017618495	78.5662	90	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287465.1	s__UBA4951 sp016287465	78.4909	109	441	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA4951	95.0	96.05	96.05	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-07-01 05:38:11,141] [INFO] GTDB search result was written to GCA_024408335.1_ASM2440833v1_genomic.fna/result_gtdb.tsv
[2023-07-01 05:38:11,142] [INFO] ===== GTDB Search completed =====
[2023-07-01 05:38:11,147] [INFO] DFAST_QC result json was written to GCA_024408335.1_ASM2440833v1_genomic.fna/dqc_result.json
[2023-07-01 05:38:11,147] [INFO] DFAST_QC completed!
[2023-07-01 05:38:11,147] [INFO] Total running time: 0h0m38s