[2023-06-29 10:06:14,825] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:06:14,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:06:14,827] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference
[2023-06-29 10:06:17,992] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:06:17,994] [INFO] Task started: Prodigal
[2023-06-29 10:06:17,994] [INFO] Running command: gunzip -c /var/lib/cwl/stgacb7ff6d-2200-4d71-a1cd-a860f2491d41/GCA_020073145.1_ASM2007314v1_genomic.fna.gz | prodigal -d GCA_020073145.1_ASM2007314v1_genomic.fna/cds.fna -a GCA_020073145.1_ASM2007314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:06:37,748] [INFO] Task succeeded: Prodigal
[2023-06-29 10:06:37,748] [INFO] Task started: HMMsearch
[2023-06-29 10:06:37,749] [INFO] Running command: hmmsearch --tblout GCA_020073145.1_ASM2007314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/reference_markers.hmm GCA_020073145.1_ASM2007314v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:06:38,101] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:06:38,102] [INFO] Found 6/6 markers.
[2023-06-29 10:06:38,156] [INFO] Query marker FASTA was written to GCA_020073145.1_ASM2007314v1_genomic.fna/markers.fasta
[2023-06-29 10:06:38,156] [INFO] Task started: Blastn
[2023-06-29 10:06:38,157] [INFO] Running command: blastn -query GCA_020073145.1_ASM2007314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/reference_markers.fasta -out GCA_020073145.1_ASM2007314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:06:38,817] [INFO] Task succeeded: Blastn
[2023-06-29 10:06:38,822] [INFO] Selected 27 target genomes.
[2023-06-29 10:06:38,823] [INFO] Target genome list was writen to GCA_020073145.1_ASM2007314v1_genomic.fna/target_genomes.txt
[2023-06-29 10:06:38,828] [INFO] Task started: fastANI
[2023-06-29 10:06:38,828] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb7ff6d-2200-4d71-a1cd-a860f2491d41/GCA_020073145.1_ASM2007314v1_genomic.fna.gz --refList GCA_020073145.1_ASM2007314v1_genomic.fna/target_genomes.txt --output GCA_020073145.1_ASM2007314v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:06:56,651] [INFO] Task succeeded: fastANI
[2023-06-29 10:06:56,652] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:06:56,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:06:56,666] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:06:56,666] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:06:56,666] [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
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	75.4904	66	2064	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	74.947	51	2064	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	74.8807	52	2064	95	below_threshold
Brevundimonas lutea	strain=NS26	GCA_003704105.1	2293980	2293980	type	True	74.7609	50	2064	95	below_threshold
Caballeronia pedi		GCA_001544915.2	1777141	1777141	type	True	74.7251	54	2064	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	74.7148	73	2064	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:06:56,673] [INFO] DFAST Taxonomy check result was written to GCA_020073145.1_ASM2007314v1_genomic.fna/tc_result.tsv
[2023-06-29 10:06:56,674] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:06:56,674] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:06:56,675] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/checkm_data
[2023-06-29 10:06:56,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:06:56,740] [INFO] Task started: CheckM
[2023-06-29 10:06:56,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020073145.1_ASM2007314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020073145.1_ASM2007314v1_genomic.fna/checkm_input GCA_020073145.1_ASM2007314v1_genomic.fna/checkm_result
[2023-06-29 10:07:50,933] [INFO] Task succeeded: CheckM
[2023-06-29 10:07:50,935] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:07:50,961] [INFO] ===== Completeness check finished =====
[2023-06-29 10:07:50,961] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:07:50,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020073145.1_ASM2007314v1_genomic.fna/markers.fasta)
[2023-06-29 10:07:50,962] [INFO] Task started: Blastn
[2023-06-29 10:07:50,962] [INFO] Running command: blastn -query GCA_020073145.1_ASM2007314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf452b01-a0ba-4a17-a0f6-ae02d1d4070f/dqc_reference/reference_markers_gtdb.fasta -out GCA_020073145.1_ASM2007314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:07:51,852] [INFO] Task succeeded: Blastn
[2023-06-29 10:07:51,858] [INFO] Selected 18 target genomes.
[2023-06-29 10:07:51,858] [INFO] Target genome list was writen to GCA_020073145.1_ASM2007314v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:07:51,867] [INFO] Task started: fastANI
[2023-06-29 10:07:51,868] [INFO] Running command: fastANI --query /var/lib/cwl/stgacb7ff6d-2200-4d71-a1cd-a860f2491d41/GCA_020073145.1_ASM2007314v1_genomic.fna.gz --refList GCA_020073145.1_ASM2007314v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020073145.1_ASM2007314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:08:08,120] [INFO] Task succeeded: fastANI
[2023-06-29 10:08:08,135] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 10:08:08,136] [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_017883415.1	s__JADGNR01 sp017883415	77.7189	395	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__JADGNR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903882645.1	s__BOG-224 sp903882645	77.2864	307	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142355.1	s__Fen-178 sp003142355	77.2433	375	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Fen-178	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003167255.1	s__PALSA-129 sp003167255	77.0948	375	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003170915.1	s__Fen-178 sp003170915	77.0797	340	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Fen-178	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003142185.1	s__Bog-375 sp003142185	77.0507	339	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Bog-375	95.0	99.72	98.50	0.96	0.85	24	-
GCA_003139735.1	s__BOG-224 sp003139735	76.9833	238	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__BOG-224	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018268835.1	s__Solibacter sp018268835	76.9827	376	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003136215.1	s__Solibacter sp003136215	76.8327	298	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	99.46	99.46	0.86	0.86	2	-
GCF_900290315.1	s__Sulfopaludibacter sp900290315	76.8158	294	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Sulfopaludibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003175985.1	s__PSRJ01 sp003175985	76.7913	331	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PSRJ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003152325.1	s__PALSA-129 sp003152325	76.768	309	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__PALSA-129	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883345.1	s__Solibacter sp017883345	76.7348	259	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Bryobacterales;f__Bryobacteraceae;g__Solibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691245.1	s__SHUM01 sp009691245	75.447	58	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__2-12-FULL-54-10;f__2-12-FULL-54-10;g__SHUM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003140075.1	s__Sulfotelmatobacter sp003140075	75.1799	55	2064	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__SbA1;g__Sulfotelmatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:08:08,138] [INFO] GTDB search result was written to GCA_020073145.1_ASM2007314v1_genomic.fna/result_gtdb.tsv
[2023-06-29 10:08:08,139] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:08:08,143] [INFO] DFAST_QC result json was written to GCA_020073145.1_ASM2007314v1_genomic.fna/dqc_result.json
[2023-06-29 10:08:08,143] [INFO] DFAST_QC completed!
[2023-06-29 10:08:08,143] [INFO] Total running time: 0h1m53s