[2023-06-26 21:35:41,069] [INFO] DFAST_QC pipeline started.
[2023-06-26 21:35:41,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 21:35:41,073] [INFO] DQC Reference Directory: /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference
[2023-06-26 21:35:42,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 21:35:42,166] [INFO] Task started: Prodigal
[2023-06-26 21:35:42,166] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d3a9290-6412-4e1d-a63c-998935fac7b7/GCA_026401035.1_ASM2640103v1_genomic.fna.gz | prodigal -d GCA_026401035.1_ASM2640103v1_genomic.fna/cds.fna -a GCA_026401035.1_ASM2640103v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 21:35:52,323] [INFO] Task succeeded: Prodigal
[2023-06-26 21:35:52,324] [INFO] Task started: HMMsearch
[2023-06-26 21:35:52,324] [INFO] Running command: hmmsearch --tblout GCA_026401035.1_ASM2640103v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/reference_markers.hmm GCA_026401035.1_ASM2640103v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 21:35:52,534] [INFO] Task succeeded: HMMsearch
[2023-06-26 21:35:52,535] [INFO] Found 6/6 markers.
[2023-06-26 21:35:52,565] [INFO] Query marker FASTA was written to GCA_026401035.1_ASM2640103v1_genomic.fna/markers.fasta
[2023-06-26 21:35:52,565] [INFO] Task started: Blastn
[2023-06-26 21:35:52,565] [INFO] Running command: blastn -query GCA_026401035.1_ASM2640103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/reference_markers.fasta -out GCA_026401035.1_ASM2640103v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:35:53,134] [INFO] Task succeeded: Blastn
[2023-06-26 21:35:53,138] [INFO] Selected 21 target genomes.
[2023-06-26 21:35:53,138] [INFO] Target genome list was writen to GCA_026401035.1_ASM2640103v1_genomic.fna/target_genomes.txt
[2023-06-26 21:35:53,140] [INFO] Task started: fastANI
[2023-06-26 21:35:53,140] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3a9290-6412-4e1d-a63c-998935fac7b7/GCA_026401035.1_ASM2640103v1_genomic.fna.gz --refList GCA_026401035.1_ASM2640103v1_genomic.fna/target_genomes.txt --output GCA_026401035.1_ASM2640103v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 21:36:15,280] [INFO] Task succeeded: fastANI
[2023-06-26 21:36:15,281] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 21:36:15,282] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 21:36:15,292] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 21:36:15,292] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 21:36:15,293] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.5157	129	1217	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.2282	120	1217	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.1909	120	1217	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.1245	163	1217	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	76.1086	67	1217	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.1041	138	1217	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.0625	124	1217	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.757	112	1217	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.3459	164	1217	95	below_threshold
Roseiconus nitratireducens	strain=JC645	GCA_008629675.1	2605748	2605748	type	True	75.3157	53	1217	95	below_threshold
Burkholderia mallei	strain=ATCC 23344	GCA_000011705.1	13373	13373	type	True	74.9432	83	1217	95	below_threshold
Burkholderia pseudomallei	strain=ATCC 23343	GCA_001182285.1	28450	28450	type	True	74.9186	95	1217	95	below_threshold
Burkholderia ubonensis subsp. mesacidophila	strain=ATCC 31433	GCA_002362295.1	265293	101571	type	True	74.8718	90	1217	95	below_threshold
Paraburkholderia caballeronis	strain=LMG 26416	GCA_900109675.1	416943	416943	type	True	74.7989	85	1217	95	below_threshold
Paraburkholderia caballeronis	strain=TNe-841	GCA_900104845.1	416943	416943	type	True	74.7982	85	1217	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.7089	86	1217	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 21:36:15,294] [INFO] DFAST Taxonomy check result was written to GCA_026401035.1_ASM2640103v1_genomic.fna/tc_result.tsv
[2023-06-26 21:36:15,295] [INFO] ===== Taxonomy check completed =====
[2023-06-26 21:36:15,295] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 21:36:15,295] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/checkm_data
[2023-06-26 21:36:15,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 21:36:15,334] [INFO] Task started: CheckM
[2023-06-26 21:36:15,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026401035.1_ASM2640103v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026401035.1_ASM2640103v1_genomic.fna/checkm_input GCA_026401035.1_ASM2640103v1_genomic.fna/checkm_result
[2023-06-26 21:36:51,942] [INFO] Task succeeded: CheckM
[2023-06-26 21:36:51,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 21:36:51,963] [INFO] ===== Completeness check finished =====
[2023-06-26 21:36:51,963] [INFO] ===== Start GTDB Search =====
[2023-06-26 21:36:51,965] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026401035.1_ASM2640103v1_genomic.fna/markers.fasta)
[2023-06-26 21:36:51,965] [INFO] Task started: Blastn
[2023-06-26 21:36:51,965] [INFO] Running command: blastn -query GCA_026401035.1_ASM2640103v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd52e5ebf-dc47-4f88-9c17-888a0d297438/dqc_reference/reference_markers_gtdb.fasta -out GCA_026401035.1_ASM2640103v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 21:36:52,834] [INFO] Task succeeded: Blastn
[2023-06-26 21:36:52,837] [INFO] Selected 16 target genomes.
[2023-06-26 21:36:52,838] [INFO] Target genome list was writen to GCA_026401035.1_ASM2640103v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 21:36:52,843] [INFO] Task started: fastANI
[2023-06-26 21:36:52,843] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d3a9290-6412-4e1d-a63c-998935fac7b7/GCA_026401035.1_ASM2640103v1_genomic.fna.gz --refList GCA_026401035.1_ASM2640103v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026401035.1_ASM2640103v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 21:37:03,626] [INFO] Task succeeded: fastANI
[2023-06-26 21:37:03,640] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 21:37:03,641] [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_010027105.1	s__RGVT01 sp010027105	80.3977	425	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	80.2489	480	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	80.0053	383	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	79.6632	405	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	79.5742	476	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670825.1	s__QWPN01 sp003670825	79.4891	290	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	79.3169	252	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	79.2614	523	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	79.2446	382	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_016872925.1	s__QWPN01 sp016872925	79.2122	475	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	79.1606	434	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_005789975.1	s__QWPN01 sp005789975	79.1369	391	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_003671185.1	s__QWPN01 sp003671185	79.0985	418	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951635.1	s__QWOP01 sp903951635	78.3232	443	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_903949225.1	s__QWOP01 sp903949225	78.1325	339	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885565.1	s__CAISJI01 sp903885565	78.0394	412	1217	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__CAISJI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 21:37:03,643] [INFO] GTDB search result was written to GCA_026401035.1_ASM2640103v1_genomic.fna/result_gtdb.tsv
[2023-06-26 21:37:03,643] [INFO] ===== GTDB Search completed =====
[2023-06-26 21:37:03,647] [INFO] DFAST_QC result json was written to GCA_026401035.1_ASM2640103v1_genomic.fna/dqc_result.json
[2023-06-26 21:37:03,647] [INFO] DFAST_QC completed!
[2023-06-26 21:37:03,647] [INFO] Total running time: 0h1m23s