[2023-06-29 21:38:49,471] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:38:49,473] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:38:49,474] [INFO] DQC Reference Directory: /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference
[2023-06-29 21:38:50,693] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:38:50,694] [INFO] Task started: Prodigal
[2023-06-29 21:38:50,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7e40754-acc4-4b1d-b550-5b3e59dcc230/GCA_016708425.1_ASM1670842v1_genomic.fna.gz | prodigal -d GCA_016708425.1_ASM1670842v1_genomic.fna/cds.fna -a GCA_016708425.1_ASM1670842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:39:26,295] [INFO] Task succeeded: Prodigal
[2023-06-29 21:39:26,295] [INFO] Task started: HMMsearch
[2023-06-29 21:39:26,295] [INFO] Running command: hmmsearch --tblout GCA_016708425.1_ASM1670842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/reference_markers.hmm GCA_016708425.1_ASM1670842v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:39:26,586] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:39:26,588] [INFO] Found 6/6 markers.
[2023-06-29 21:39:26,631] [INFO] Query marker FASTA was written to GCA_016708425.1_ASM1670842v1_genomic.fna/markers.fasta
[2023-06-29 21:39:26,632] [INFO] Task started: Blastn
[2023-06-29 21:39:26,632] [INFO] Running command: blastn -query GCA_016708425.1_ASM1670842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/reference_markers.fasta -out GCA_016708425.1_ASM1670842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:39:27,243] [INFO] Task succeeded: Blastn
[2023-06-29 21:39:27,249] [INFO] Selected 35 target genomes.
[2023-06-29 21:39:27,249] [INFO] Target genome list was writen to GCA_016708425.1_ASM1670842v1_genomic.fna/target_genomes.txt
[2023-06-29 21:39:27,255] [INFO] Task started: fastANI
[2023-06-29 21:39:27,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7e40754-acc4-4b1d-b550-5b3e59dcc230/GCA_016708425.1_ASM1670842v1_genomic.fna.gz --refList GCA_016708425.1_ASM1670842v1_genomic.fna/target_genomes.txt --output GCA_016708425.1_ASM1670842v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:39:50,637] [INFO] Task succeeded: fastANI
[2023-06-29 21:39:50,638] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:39:50,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:39:50,647] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:39:50,647] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 21:39:50,647] [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
Hymenobacter armeniacus	strain=BT189	GCA_014699055.1	2771358	2771358	type	True	75.8407	56	1553	95	below_threshold
Hymenobacter edaphi	strain=NL	GCA_003258365.1	2211146	2211146	type	True	75.8015	58	1553	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 21:39:50,655] [INFO] DFAST Taxonomy check result was written to GCA_016708425.1_ASM1670842v1_genomic.fna/tc_result.tsv
[2023-06-29 21:39:50,656] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:39:50,656] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:39:50,657] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/checkm_data
[2023-06-29 21:39:50,659] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:39:50,702] [INFO] Task started: CheckM
[2023-06-29 21:39:50,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708425.1_ASM1670842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708425.1_ASM1670842v1_genomic.fna/checkm_input GCA_016708425.1_ASM1670842v1_genomic.fna/checkm_result
[2023-06-29 21:41:22,264] [INFO] Task succeeded: CheckM
[2023-06-29 21:41:22,266] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 21:41:22,290] [INFO] ===== Completeness check finished =====
[2023-06-29 21:41:22,291] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:41:22,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708425.1_ASM1670842v1_genomic.fna/markers.fasta)
[2023-06-29 21:41:22,291] [INFO] Task started: Blastn
[2023-06-29 21:41:22,292] [INFO] Running command: blastn -query GCA_016708425.1_ASM1670842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6cc84e37-ef4f-4390-93c1-29935ee82004/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708425.1_ASM1670842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:41:23,117] [INFO] Task succeeded: Blastn
[2023-06-29 21:41:23,122] [INFO] Selected 17 target genomes.
[2023-06-29 21:41:23,122] [INFO] Target genome list was writen to GCA_016708425.1_ASM1670842v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:41:23,130] [INFO] Task started: fastANI
[2023-06-29 21:41:23,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7e40754-acc4-4b1d-b550-5b3e59dcc230/GCA_016708425.1_ASM1670842v1_genomic.fna.gz --refList GCA_016708425.1_ASM1670842v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708425.1_ASM1670842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:41:37,126] [INFO] Task succeeded: fastANI
[2023-06-29 21:41:37,145] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:41:37,145] [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_016703105.1	s__PHOS-HE28 sp016703105	98.5276	1397	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	98.92	98.53	0.94	0.90	7	conclusive
GCA_017987895.1	s__PHOS-HE28 sp017987895	93.3049	1011	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.66	0.85	0.85	2	-
GCA_016712025.1	s__PHOS-HE28 sp016712025	87.0867	989	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016702645.1	s__PHOS-HE28 sp016702645	80.6454	425	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715895.1	s__PHOS-HE28 sp016715895	79.8088	589	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713875.1	s__PHOS-HE28 sp016713875	79.7177	594	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.66	99.38	0.97	0.94	4	-
GCA_013360395.1	s__PHOS-HE28 sp013360395	79.4995	508	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.56	99.56	0.97	0.97	2	-
GCA_014584605.1	s__PHOS-HE28 sp014584605	79.3271	503	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788285.1	s__PHOS-HE28 sp016788285	79.3258	478	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018267055.1	s__PHOS-HE28 sp018267055	79.1428	417	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788635.1	s__PHOS-HE28 sp016788635	78.9961	375	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788205.1	s__PHOS-HE28 sp016788205	78.6781	370	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788295.1	s__PHOS-HE28 sp016788295	78.6444	357	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008016945.1	s__PHOS-HE28 sp008016945	78.5549	323	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016717305.1	s__PHOS-HE28 sp016717305	78.2838	243	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.11	99.05	0.96	0.96	3	-
GCA_018267065.1	s__PHOS-HE28 sp018267065	78.1555	226	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700415.1	s__PHOS-HE28 sp002396605	78.1288	324	1553	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__PHOS-HE28;g__PHOS-HE28	95.0	99.63	99.43	0.98	0.96	12	-
--------------------------------------------------------------------------------
[2023-06-29 21:41:37,148] [INFO] GTDB search result was written to GCA_016708425.1_ASM1670842v1_genomic.fna/result_gtdb.tsv
[2023-06-29 21:41:37,148] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:41:37,153] [INFO] DFAST_QC result json was written to GCA_016708425.1_ASM1670842v1_genomic.fna/dqc_result.json
[2023-06-29 21:41:37,153] [INFO] DFAST_QC completed!
[2023-06-29 21:41:37,153] [INFO] Total running time: 0h2m48s