[2023-06-13 01:40:34,824] [INFO] DFAST_QC pipeline started.
[2023-06-13 01:40:34,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 01:40:34,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference
[2023-06-13 01:40:37,895] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 01:40:37,897] [INFO] Task started: Prodigal
[2023-06-13 01:40:37,897] [INFO] Running command: gunzip -c /var/lib/cwl/stgf9b652d6-a608-4657-b685-fba89c423096/GCA_022571925.1_ASM2257192v1_genomic.fna.gz | prodigal -d GCA_022571925.1_ASM2257192v1_genomic.fna/cds.fna -a GCA_022571925.1_ASM2257192v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 01:40:46,528] [INFO] Task succeeded: Prodigal
[2023-06-13 01:40:46,531] [INFO] Task started: HMMsearch
[2023-06-13 01:40:46,531] [INFO] Running command: hmmsearch --tblout GCA_022571925.1_ASM2257192v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/reference_markers.hmm GCA_022571925.1_ASM2257192v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 01:40:46,773] [INFO] Task succeeded: HMMsearch
[2023-06-13 01:40:46,775] [INFO] Found 6/6 markers.
[2023-06-13 01:40:46,816] [INFO] Query marker FASTA was written to GCA_022571925.1_ASM2257192v1_genomic.fna/markers.fasta
[2023-06-13 01:40:46,817] [INFO] Task started: Blastn
[2023-06-13 01:40:46,817] [INFO] Running command: blastn -query GCA_022571925.1_ASM2257192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/reference_markers.fasta -out GCA_022571925.1_ASM2257192v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:40:47,448] [INFO] Task succeeded: Blastn
[2023-06-13 01:40:47,453] [INFO] Selected 24 target genomes.
[2023-06-13 01:40:47,454] [INFO] Target genome list was writen to GCA_022571925.1_ASM2257192v1_genomic.fna/target_genomes.txt
[2023-06-13 01:40:47,459] [INFO] Task started: fastANI
[2023-06-13 01:40:47,459] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b652d6-a608-4657-b685-fba89c423096/GCA_022571925.1_ASM2257192v1_genomic.fna.gz --refList GCA_022571925.1_ASM2257192v1_genomic.fna/target_genomes.txt --output GCA_022571925.1_ASM2257192v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 01:41:05,303] [INFO] Task succeeded: fastANI
[2023-06-13 01:41:05,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 01:41:05,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 01:41:05,312] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 01:41:05,312] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 01:41:05,312] [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
Azospirillum rugosum	strain=IMMIB AFH-6	GCA_017876155.1	416170	416170	type	True	74.836	58	851	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.8131	60	851	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 01:41:05,321] [INFO] DFAST Taxonomy check result was written to GCA_022571925.1_ASM2257192v1_genomic.fna/tc_result.tsv
[2023-06-13 01:41:05,323] [INFO] ===== Taxonomy check completed =====
[2023-06-13 01:41:05,324] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 01:41:05,324] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/checkm_data
[2023-06-13 01:41:05,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 01:41:05,370] [INFO] Task started: CheckM
[2023-06-13 01:41:05,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022571925.1_ASM2257192v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022571925.1_ASM2257192v1_genomic.fna/checkm_input GCA_022571925.1_ASM2257192v1_genomic.fna/checkm_result
[2023-06-13 01:41:34,421] [INFO] Task succeeded: CheckM
[2023-06-13 01:41:34,423] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.25%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 01:41:34,451] [INFO] ===== Completeness check finished =====
[2023-06-13 01:41:34,451] [INFO] ===== Start GTDB Search =====
[2023-06-13 01:41:34,452] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022571925.1_ASM2257192v1_genomic.fna/markers.fasta)
[2023-06-13 01:41:34,452] [INFO] Task started: Blastn
[2023-06-13 01:41:34,452] [INFO] Running command: blastn -query GCA_022571925.1_ASM2257192v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf40ed28d-deb6-4b58-a003-4bbcb236fcfc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022571925.1_ASM2257192v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 01:41:35,408] [INFO] Task succeeded: Blastn
[2023-06-13 01:41:35,413] [INFO] Selected 14 target genomes.
[2023-06-13 01:41:35,414] [INFO] Target genome list was writen to GCA_022571925.1_ASM2257192v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 01:41:35,419] [INFO] Task started: fastANI
[2023-06-13 01:41:35,419] [INFO] Running command: fastANI --query /var/lib/cwl/stgf9b652d6-a608-4657-b685-fba89c423096/GCA_022571925.1_ASM2257192v1_genomic.fna.gz --refList GCA_022571925.1_ASM2257192v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022571925.1_ASM2257192v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 01:41:45,824] [INFO] Task succeeded: fastANI
[2023-06-13 01:41:45,837] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 01:41:45,837] [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_903914415.1	s__Fen-1342 sp903914415	76.8449	95	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__Fen-1342	95.0	99.57	99.48	0.90	0.90	3	-
GCA_900696525.1	s__CAADGL01 sp900696525	76.8129	133	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__CAADGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900696535.1	s__CAADGM01 sp900696535	76.6408	82	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__CAADGM01	95.0	99.20	99.20	0.91	0.91	2	-
GCA_007859745.1	s__RAS1 sp007859745	76.5867	117	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__RAS1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017999985.1	s__JAGNKU01 sp017999985	76.5784	115	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAGNKU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709575.1	s__H1-PLA3 sp015709575	76.5453	69	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__H1-PLA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003162245.1	s__Fen-1342 sp003162245	76.4781	126	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__Fen-1342	95.0	99.89	99.89	0.96	0.96	2	-
GCA_016710275.1	s__H1-PLA3 sp016710275	76.4437	85	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__H1-PLA3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011054455.1	s__DSPM01 sp011054455	76.432	138	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__DSPM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235145.1	s__JACRLV01 sp016235145	76.3733	67	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JACRLV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056925.1	s__JAAYXS01 sp018056925	76.3034	54	851	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__UBA1845;f__Fen-1342;g__JAAYXS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 01:41:45,839] [INFO] GTDB search result was written to GCA_022571925.1_ASM2257192v1_genomic.fna/result_gtdb.tsv
[2023-06-13 01:41:45,840] [INFO] ===== GTDB Search completed =====
[2023-06-13 01:41:45,846] [INFO] DFAST_QC result json was written to GCA_022571925.1_ASM2257192v1_genomic.fna/dqc_result.json
[2023-06-13 01:41:45,846] [INFO] DFAST_QC completed!
[2023-06-13 01:41:45,846] [INFO] Total running time: 0h1m11s