[2023-06-28 16:42:53,982] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:42:53,985] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:42:53,985] [INFO] DQC Reference Directory: /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference
[2023-06-28 16:42:55,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:42:55,402] [INFO] Task started: Prodigal
[2023-06-28 16:42:55,402] [INFO] Running command: gunzip -c /var/lib/cwl/stga5bb8897-60bf-4147-a0d5-9c588eda6eb9/GCA_017965685.1_ASM1796568v1_genomic.fna.gz | prodigal -d GCA_017965685.1_ASM1796568v1_genomic.fna/cds.fna -a GCA_017965685.1_ASM1796568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:42:58,827] [INFO] Task succeeded: Prodigal
[2023-06-28 16:42:58,827] [INFO] Task started: HMMsearch
[2023-06-28 16:42:58,827] [INFO] Running command: hmmsearch --tblout GCA_017965685.1_ASM1796568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/reference_markers.hmm GCA_017965685.1_ASM1796568v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:42:59,029] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:42:59,031] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga5bb8897-60bf-4147-a0d5-9c588eda6eb9/GCA_017965685.1_ASM1796568v1_genomic.fna.gz]
[2023-06-28 16:42:59,050] [INFO] Query marker FASTA was written to GCA_017965685.1_ASM1796568v1_genomic.fna/markers.fasta
[2023-06-28 16:42:59,051] [INFO] Task started: Blastn
[2023-06-28 16:42:59,051] [INFO] Running command: blastn -query GCA_017965685.1_ASM1796568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/reference_markers.fasta -out GCA_017965685.1_ASM1796568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:42:59,543] [INFO] Task succeeded: Blastn
[2023-06-28 16:42:59,547] [INFO] Selected 12 target genomes.
[2023-06-28 16:42:59,547] [INFO] Target genome list was writen to GCA_017965685.1_ASM1796568v1_genomic.fna/target_genomes.txt
[2023-06-28 16:42:59,553] [INFO] Task started: fastANI
[2023-06-28 16:42:59,553] [INFO] Running command: fastANI --query /var/lib/cwl/stga5bb8897-60bf-4147-a0d5-9c588eda6eb9/GCA_017965685.1_ASM1796568v1_genomic.fna.gz --refList GCA_017965685.1_ASM1796568v1_genomic.fna/target_genomes.txt --output GCA_017965685.1_ASM1796568v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:43:10,162] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:10,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:43:10,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:43:10,168] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 16:43:10,168] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 16:43:10,169] [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 16:43:10,170] [INFO] DFAST Taxonomy check result was written to GCA_017965685.1_ASM1796568v1_genomic.fna/tc_result.tsv
[2023-06-28 16:43:10,171] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:43:10,171] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:43:10,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/checkm_data
[2023-06-28 16:43:10,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:43:10,193] [INFO] Task started: CheckM
[2023-06-28 16:43:10,194] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017965685.1_ASM1796568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017965685.1_ASM1796568v1_genomic.fna/checkm_input GCA_017965685.1_ASM1796568v1_genomic.fna/checkm_result
[2023-06-28 16:43:28,733] [INFO] Task succeeded: CheckM
[2023-06-28 16:43:28,735] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:43:28,754] [INFO] ===== Completeness check finished =====
[2023-06-28 16:43:28,755] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:43:28,755] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017965685.1_ASM1796568v1_genomic.fna/markers.fasta)
[2023-06-28 16:43:28,755] [INFO] Task started: Blastn
[2023-06-28 16:43:28,756] [INFO] Running command: blastn -query GCA_017965685.1_ASM1796568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf852898d-fb37-491f-a7b2-fe78b831d53c/dqc_reference/reference_markers_gtdb.fasta -out GCA_017965685.1_ASM1796568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:43:29,246] [INFO] Task succeeded: Blastn
[2023-06-28 16:43:29,250] [INFO] Selected 14 target genomes.
[2023-06-28 16:43:29,250] [INFO] Target genome list was writen to GCA_017965685.1_ASM1796568v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:43:29,263] [INFO] Task started: fastANI
[2023-06-28 16:43:29,264] [INFO] Running command: fastANI --query /var/lib/cwl/stga5bb8897-60bf-4147-a0d5-9c588eda6eb9/GCA_017965685.1_ASM1796568v1_genomic.fna.gz --refList GCA_017965685.1_ASM1796568v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017965685.1_ASM1796568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:43:35,371] [INFO] Task succeeded: fastANI
[2023-06-28 16:43:35,386] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:43:35,386] [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_017965685.1	s__UBA1067 sp017965685	100.0	346	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002449695.1	s__UBA1067 sp002449695	78.5462	112	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017463935.1	s__UBA1067 sp017463935	78.5238	94	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432385.1	s__UBA1067 sp017432385	78.2303	84	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016284515.1	s__UBA1067 sp016284515	77.9903	105	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015061665.1	s__UBA1067 sp015061665	77.9377	97	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902775595.1	s__UBA1067 sp002350535	77.8138	106	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.6109	97.09	96.38	0.75	0.66	7	-
GCA_900321255.1	s__UBA1067 sp900321255	77.7571	97	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.6109	100.00	100.00	1.00	1.00	2	-
GCA_902763655.1	s__RUG572 sp902763655	77.2728	62	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__RUG572	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017650345.1	s__UBA1067 sp017650345	77.2073	82	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395905.1	s__UBA1067 sp002395905	77.0524	69	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	97.54	97.54	0.77	0.77	2	-
GCA_017508315.1	s__UBA1067 sp017508315	76.8874	51	347	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA1067;g__UBA1067	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 16:43:35,389] [INFO] GTDB search result was written to GCA_017965685.1_ASM1796568v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:43:35,390] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:43:35,393] [INFO] DFAST_QC result json was written to GCA_017965685.1_ASM1796568v1_genomic.fna/dqc_result.json
[2023-06-28 16:43:35,393] [INFO] DFAST_QC completed!
[2023-06-28 16:43:35,393] [INFO] Total running time: 0h0m41s