[2023-06-07 21:13:30,536] [INFO] DFAST_QC pipeline started.
[2023-06-07 21:13:30,539] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 21:13:30,539] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference
[2023-06-07 21:13:33,293] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 21:13:33,294] [INFO] Task started: Prodigal
[2023-06-07 21:13:33,294] [INFO] Running command: gunzip -c /var/lib/cwl/stg2f516c34-e623-474f-966a-aafe5e1d0f69/GCA_945897435.1_MsE-01oct19-48_genomic.fna.gz | prodigal -d GCA_945897435.1_MsE-01oct19-48_genomic.fna/cds.fna -a GCA_945897435.1_MsE-01oct19-48_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 21:13:40,951] [INFO] Task succeeded: Prodigal
[2023-06-07 21:13:40,952] [INFO] Task started: HMMsearch
[2023-06-07 21:13:40,952] [INFO] Running command: hmmsearch --tblout GCA_945897435.1_MsE-01oct19-48_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/reference_markers.hmm GCA_945897435.1_MsE-01oct19-48_genomic.fna/protein.faa > /dev/null
[2023-06-07 21:13:41,226] [INFO] Task succeeded: HMMsearch
[2023-06-07 21:13:41,228] [INFO] Found 6/6 markers.
[2023-06-07 21:13:41,257] [INFO] Query marker FASTA was written to GCA_945897435.1_MsE-01oct19-48_genomic.fna/markers.fasta
[2023-06-07 21:13:41,257] [INFO] Task started: Blastn
[2023-06-07 21:13:41,257] [INFO] Running command: blastn -query GCA_945897435.1_MsE-01oct19-48_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/reference_markers.fasta -out GCA_945897435.1_MsE-01oct19-48_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:13:41,857] [INFO] Task succeeded: Blastn
[2023-06-07 21:13:41,862] [INFO] Selected 29 target genomes.
[2023-06-07 21:13:41,863] [INFO] Target genome list was writen to GCA_945897435.1_MsE-01oct19-48_genomic.fna/target_genomes.txt
[2023-06-07 21:13:41,868] [INFO] Task started: fastANI
[2023-06-07 21:13:41,869] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f516c34-e623-474f-966a-aafe5e1d0f69/GCA_945897435.1_MsE-01oct19-48_genomic.fna.gz --refList GCA_945897435.1_MsE-01oct19-48_genomic.fna/target_genomes.txt --output GCA_945897435.1_MsE-01oct19-48_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 21:14:07,248] [INFO] Task succeeded: fastANI
[2023-06-07 21:14:07,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 21:14:07,249] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 21:14:07,264] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 21:14:07,265] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 21:14:07,265] [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	76.6176	109	909	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	76.3082	89	909	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.3057	123	909	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	76.2658	102	909	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.1404	112	909	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.1269	93	909	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.8853	79	909	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.3658	100	909	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.3613	124	909	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 21:14:07,267] [INFO] DFAST Taxonomy check result was written to GCA_945897435.1_MsE-01oct19-48_genomic.fna/tc_result.tsv
[2023-06-07 21:14:07,267] [INFO] ===== Taxonomy check completed =====
[2023-06-07 21:14:07,268] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 21:14:07,268] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/checkm_data
[2023-06-07 21:14:07,269] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 21:14:07,302] [INFO] Task started: CheckM
[2023-06-07 21:14:07,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945897435.1_MsE-01oct19-48_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945897435.1_MsE-01oct19-48_genomic.fna/checkm_input GCA_945897435.1_MsE-01oct19-48_genomic.fna/checkm_result
[2023-06-07 21:14:46,379] [INFO] Task succeeded: CheckM
[2023-06-07 21:14:46,381] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 21:14:46,408] [INFO] ===== Completeness check finished =====
[2023-06-07 21:14:46,408] [INFO] ===== Start GTDB Search =====
[2023-06-07 21:14:46,408] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945897435.1_MsE-01oct19-48_genomic.fna/markers.fasta)
[2023-06-07 21:14:46,409] [INFO] Task started: Blastn
[2023-06-07 21:14:46,409] [INFO] Running command: blastn -query GCA_945897435.1_MsE-01oct19-48_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0927b6a-0b5d-499e-9383-84435d1ad939/dqc_reference/reference_markers_gtdb.fasta -out GCA_945897435.1_MsE-01oct19-48_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 21:14:47,250] [INFO] Task succeeded: Blastn
[2023-06-07 21:14:47,256] [INFO] Selected 21 target genomes.
[2023-06-07 21:14:47,256] [INFO] Target genome list was writen to GCA_945897435.1_MsE-01oct19-48_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 21:14:47,263] [INFO] Task started: fastANI
[2023-06-07 21:14:47,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg2f516c34-e623-474f-966a-aafe5e1d0f69/GCA_945897435.1_MsE-01oct19-48_genomic.fna.gz --refList GCA_945897435.1_MsE-01oct19-48_genomic.fna/target_genomes_gtdb.txt --output GCA_945897435.1_MsE-01oct19-48_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 21:15:00,435] [INFO] Task succeeded: fastANI
[2023-06-07 21:15:00,462] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 21:15:00,463] [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_009926295.1	s__RGVT01 sp009926295	79.9445	423	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	79.5932	383	909	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	79.5257	337	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	79.4668	337	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	79.4366	418	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	79.4253	419	909	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	79.3837	440	909	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	79.2631	252	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405515.1	s__UBA4655 sp002405515	79.1618	358	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669255.1	s__QWPN01 sp003669255	79.0836	238	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	78.9899	337	909	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	78.8576	317	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_903885855.1	s__QWOP01 sp903885855	78.8231	342	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903951635.1	s__QWOP01 sp903951635	78.7733	400	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	99.54	99.51	0.90	0.90	3	-
GCA_903919035.1	s__QWPN01 sp903919035	78.6701	367	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_017853835.1	s__QWPN01 sp017853835	78.4982	331	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691925.1	s__QWOP01 sp009691925	78.2454	259	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003669605.1	s__QWOP01 sp003669605	77.9247	273	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016936015.1	s__JAFGPV01 sp016936015	76.0523	79	909	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Thermoguttaceae;g__JAFGPV01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 21:15:00,478] [INFO] GTDB search result was written to GCA_945897435.1_MsE-01oct19-48_genomic.fna/result_gtdb.tsv
[2023-06-07 21:15:00,479] [INFO] ===== GTDB Search completed =====
[2023-06-07 21:15:00,485] [INFO] DFAST_QC result json was written to GCA_945897435.1_MsE-01oct19-48_genomic.fna/dqc_result.json
[2023-06-07 21:15:00,486] [INFO] DFAST_QC completed!
[2023-06-07 21:15:00,486] [INFO] Total running time: 0h1m30s