[2023-06-28 10:22:07,851] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:22:07,858] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:22:07,858] [INFO] DQC Reference Directory: /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference
[2023-06-28 10:22:10,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:22:10,410] [INFO] Task started: Prodigal
[2023-06-28 10:22:10,410] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b3cba4b-fd64-4584-b777-cdc61d137d9f/GCA_017856715.1_ASM1785671v1_genomic.fna.gz | prodigal -d GCA_017856715.1_ASM1785671v1_genomic.fna/cds.fna -a GCA_017856715.1_ASM1785671v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:22:17,646] [INFO] Task succeeded: Prodigal
[2023-06-28 10:22:17,646] [INFO] Task started: HMMsearch
[2023-06-28 10:22:17,646] [INFO] Running command: hmmsearch --tblout GCA_017856715.1_ASM1785671v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/reference_markers.hmm GCA_017856715.1_ASM1785671v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:22:17,957] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:22:17,959] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3b3cba4b-fd64-4584-b777-cdc61d137d9f/GCA_017856715.1_ASM1785671v1_genomic.fna.gz]
[2023-06-28 10:22:17,988] [INFO] Query marker FASTA was written to GCA_017856715.1_ASM1785671v1_genomic.fna/markers.fasta
[2023-06-28 10:22:17,988] [INFO] Task started: Blastn
[2023-06-28 10:22:17,988] [INFO] Running command: blastn -query GCA_017856715.1_ASM1785671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/reference_markers.fasta -out GCA_017856715.1_ASM1785671v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:22:19,612] [INFO] Task succeeded: Blastn
[2023-06-28 10:22:19,617] [INFO] Selected 23 target genomes.
[2023-06-28 10:22:19,617] [INFO] Target genome list was writen to GCA_017856715.1_ASM1785671v1_genomic.fna/target_genomes.txt
[2023-06-28 10:22:19,638] [INFO] Task started: fastANI
[2023-06-28 10:22:19,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b3cba4b-fd64-4584-b777-cdc61d137d9f/GCA_017856715.1_ASM1785671v1_genomic.fna.gz --refList GCA_017856715.1_ASM1785671v1_genomic.fna/target_genomes.txt --output GCA_017856715.1_ASM1785671v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:22:36,994] [INFO] Task succeeded: fastANI
[2023-06-28 10:22:36,995] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:22:36,995] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:22:37,003] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:22:37,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 10:22:37,003] [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
Steroidobacter agariperforans	strain=KA5-B	GCA_004138335.1	268404	268404	type	True	76.2344	84	696	95	below_threshold
Steroidobacter soli	strain=JW-3	GCA_004138485.1	2497877	2497877	type	True	76.1434	86	696	95	below_threshold
Steroidobacter agaridevorans	strain=SA29-B	GCA_009932555.1	2695856	2695856	type	True	76.1208	89	696	95	below_threshold
Lysobacter segetis	strain=17J68-2	GCA_004359965.1	2492394	2492394	type	True	75.9695	51	696	95	below_threshold
Sphaerotilus sulfidivorans	strain=D-501	GCA_013426975.1	639200	639200	type	True	75.8293	53	696	95	below_threshold
Povalibacter uvarum	strain=DSM 26723	GCA_014202975.1	732238	732238	type	True	75.8067	90	696	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.6019	76	696	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 10:22:37,005] [INFO] DFAST Taxonomy check result was written to GCA_017856715.1_ASM1785671v1_genomic.fna/tc_result.tsv
[2023-06-28 10:22:37,006] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:22:37,006] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:22:37,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/checkm_data
[2023-06-28 10:22:37,007] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:22:37,041] [INFO] Task started: CheckM
[2023-06-28 10:22:37,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017856715.1_ASM1785671v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017856715.1_ASM1785671v1_genomic.fna/checkm_input GCA_017856715.1_ASM1785671v1_genomic.fna/checkm_result
[2023-06-28 10:23:03,060] [INFO] Task succeeded: CheckM
[2023-06-28 10:23:03,062] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 10:23:03,087] [INFO] ===== Completeness check finished =====
[2023-06-28 10:23:03,088] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:23:03,088] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017856715.1_ASM1785671v1_genomic.fna/markers.fasta)
[2023-06-28 10:23:03,088] [INFO] Task started: Blastn
[2023-06-28 10:23:03,089] [INFO] Running command: blastn -query GCA_017856715.1_ASM1785671v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64ccf2be-11dc-4ec0-b991-2e20ff637966/dqc_reference/reference_markers_gtdb.fasta -out GCA_017856715.1_ASM1785671v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:23:03,847] [INFO] Task succeeded: Blastn
[2023-06-28 10:23:03,852] [INFO] Selected 10 target genomes.
[2023-06-28 10:23:03,852] [INFO] Target genome list was writen to GCA_017856715.1_ASM1785671v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:23:03,858] [INFO] Task started: fastANI
[2023-06-28 10:23:03,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b3cba4b-fd64-4584-b777-cdc61d137d9f/GCA_017856715.1_ASM1785671v1_genomic.fna.gz --refList GCA_017856715.1_ASM1785671v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017856715.1_ASM1785671v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:23:08,474] [INFO] Task succeeded: fastANI
[2023-06-28 10:23:08,484] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 10:23:08,485] [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_010031985.1	s__UBA964 sp010031985	98.6262	444	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.93	98.76	0.80	0.76	12	conclusive
GCA_016874175.1	s__UBA964 sp016874175	85.54	525	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874555.1	s__UBA964 sp016874555	83.624	470	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923475.1	s__UBA964 sp009923475	79.016	214	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885195.1	s__UBA964 sp903885195	79.0038	280	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	99.55	99.16	0.90	0.86	6	-
GCA_017853555.1	s__UBA964 sp017853555	78.4874	268	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017853175.1	s__UBA964 sp017853175	78.3587	215	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029775.1	s__UBA964 sp010029775	78.0371	212	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910215.1	s__UBA964 sp903910215	77.941	168	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	98.86	98.86	0.82	0.82	2	-
GCA_018970145.1	s__UBA964 sp018970145	77.6383	206	696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__UBA964	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:23:08,487] [INFO] GTDB search result was written to GCA_017856715.1_ASM1785671v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:23:08,489] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:23:08,493] [INFO] DFAST_QC result json was written to GCA_017856715.1_ASM1785671v1_genomic.fna/dqc_result.json
[2023-06-28 10:23:08,493] [INFO] DFAST_QC completed!
[2023-06-28 10:23:08,494] [INFO] Total running time: 0h1m1s