[2023-06-17 09:46:15,265] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:46:15,268] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:46:15,269] [INFO] DQC Reference Directory: /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference
[2023-06-17 09:46:17,292] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:46:17,293] [INFO] Task started: Prodigal
[2023-06-17 09:46:17,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b69a9de-93ad-462b-973a-b9d498fb313b/GCA_013335365.1_ASM1333536v1_genomic.fna.gz | prodigal -d GCA_013335365.1_ASM1333536v1_genomic.fna/cds.fna -a GCA_013335365.1_ASM1333536v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:46:22,871] [INFO] Task succeeded: Prodigal
[2023-06-17 09:46:22,872] [INFO] Task started: HMMsearch
[2023-06-17 09:46:22,872] [INFO] Running command: hmmsearch --tblout GCA_013335365.1_ASM1333536v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/reference_markers.hmm GCA_013335365.1_ASM1333536v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:46:23,114] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:46:23,116] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg8b69a9de-93ad-462b-973a-b9d498fb313b/GCA_013335365.1_ASM1333536v1_genomic.fna.gz]
[2023-06-17 09:46:23,146] [INFO] Query marker FASTA was written to GCA_013335365.1_ASM1333536v1_genomic.fna/markers.fasta
[2023-06-17 09:46:23,146] [INFO] Task started: Blastn
[2023-06-17 09:46:23,146] [INFO] Running command: blastn -query GCA_013335365.1_ASM1333536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/reference_markers.fasta -out GCA_013335365.1_ASM1333536v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:46:23,739] [INFO] Task succeeded: Blastn
[2023-06-17 09:46:23,745] [INFO] Selected 19 target genomes.
[2023-06-17 09:46:23,745] [INFO] Target genome list was writen to GCA_013335365.1_ASM1333536v1_genomic.fna/target_genomes.txt
[2023-06-17 09:46:23,751] [INFO] Task started: fastANI
[2023-06-17 09:46:23,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b69a9de-93ad-462b-973a-b9d498fb313b/GCA_013335365.1_ASM1333536v1_genomic.fna.gz --refList GCA_013335365.1_ASM1333536v1_genomic.fna/target_genomes.txt --output GCA_013335365.1_ASM1333536v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:46:36,437] [INFO] Task succeeded: fastANI
[2023-06-17 09:46:36,437] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:46:36,438] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:46:36,440] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:46:36,440] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:46:36,440] [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
--------------------------------------------------------------------------------
[2023-06-17 09:46:36,442] [INFO] DFAST Taxonomy check result was written to GCA_013335365.1_ASM1333536v1_genomic.fna/tc_result.tsv
[2023-06-17 09:46:36,443] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:46:36,443] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:46:36,444] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/checkm_data
[2023-06-17 09:46:36,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:46:36,482] [INFO] Task started: CheckM
[2023-06-17 09:46:36,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013335365.1_ASM1333536v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013335365.1_ASM1333536v1_genomic.fna/checkm_input GCA_013335365.1_ASM1333536v1_genomic.fna/checkm_result
[2023-06-17 09:46:59,684] [INFO] Task succeeded: CheckM
[2023-06-17 09:46:59,686] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.37%
Contamintation: 5.01%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 09:46:59,709] [INFO] ===== Completeness check finished =====
[2023-06-17 09:46:59,709] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:46:59,709] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013335365.1_ASM1333536v1_genomic.fna/markers.fasta)
[2023-06-17 09:46:59,710] [INFO] Task started: Blastn
[2023-06-17 09:46:59,710] [INFO] Running command: blastn -query GCA_013335365.1_ASM1333536v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba31de69-0e02-4000-bbc6-0f25570acc41/dqc_reference/reference_markers_gtdb.fasta -out GCA_013335365.1_ASM1333536v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:47:00,565] [INFO] Task succeeded: Blastn
[2023-06-17 09:47:00,570] [INFO] Selected 17 target genomes.
[2023-06-17 09:47:00,570] [INFO] Target genome list was writen to GCA_013335365.1_ASM1333536v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:47:00,586] [INFO] Task started: fastANI
[2023-06-17 09:47:00,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b69a9de-93ad-462b-973a-b9d498fb313b/GCA_013335365.1_ASM1333536v1_genomic.fna.gz --refList GCA_013335365.1_ASM1333536v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013335365.1_ASM1333536v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:47:11,197] [INFO] Task succeeded: fastANI
[2023-06-17 09:47:11,205] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:47:11,205] [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_013360875.1	s__UBA12294 sp013360875	79.6925	163	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016223135.1	s__UBA12294 sp016223135	79.268	133	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.98	99.98	0.97	0.97	2	-
GCA_013388685.1	s__UBA12294 sp013388685	79.2636	149	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002418205.1	s__UBA12294 sp002418205	79.1832	143	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.83	99.80	0.91	0.90	3	-
GCA_016721115.1	s__UBA12294 sp016721115	78.2315	100	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011331405.1	s__UBA12294 sp011331405	78.1375	96	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	99.98	99.98	0.99	0.99	2	-
GCA_003577395.1	s__UBA12294 sp003577395	77.685	57	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	95.23	95.23	0.89	0.89	2	-
GCA_003484265.1	s__UBA12294 sp003484265	77.2719	62	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932715.1	s__UBA12294 sp016932715	77.2386	74	328	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__EnvOPS12;g__UBA12294	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:47:11,208] [INFO] GTDB search result was written to GCA_013335365.1_ASM1333536v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:47:11,208] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:47:11,211] [INFO] DFAST_QC result json was written to GCA_013335365.1_ASM1333536v1_genomic.fna/dqc_result.json
[2023-06-17 09:47:11,211] [INFO] DFAST_QC completed!
[2023-06-17 09:47:11,211] [INFO] Total running time: 0h0m56s