[2023-06-08 13:03:06,990] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:03:06,993] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:03:06,994] [INFO] DQC Reference Directory: /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference
[2023-06-08 13:03:08,411] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:03:08,414] [INFO] Task started: Prodigal
[2023-06-08 13:03:08,415] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc0350e2-1442-474c-8b40-86868384604a/GCA_945877135.1_MiE-14oct19-235_genomic.fna.gz | prodigal -d GCA_945877135.1_MiE-14oct19-235_genomic.fna/cds.fna -a GCA_945877135.1_MiE-14oct19-235_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:03:19,904] [INFO] Task succeeded: Prodigal
[2023-06-08 13:03:19,904] [INFO] Task started: HMMsearch
[2023-06-08 13:03:19,905] [INFO] Running command: hmmsearch --tblout GCA_945877135.1_MiE-14oct19-235_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/reference_markers.hmm GCA_945877135.1_MiE-14oct19-235_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:03:20,185] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:03:20,186] [INFO] Found 6/6 markers.
[2023-06-08 13:03:20,230] [INFO] Query marker FASTA was written to GCA_945877135.1_MiE-14oct19-235_genomic.fna/markers.fasta
[2023-06-08 13:03:20,231] [INFO] Task started: Blastn
[2023-06-08 13:03:20,231] [INFO] Running command: blastn -query GCA_945877135.1_MiE-14oct19-235_genomic.fna/markers.fasta -db /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/reference_markers.fasta -out GCA_945877135.1_MiE-14oct19-235_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:03:20,918] [INFO] Task succeeded: Blastn
[2023-06-08 13:03:20,923] [INFO] Selected 20 target genomes.
[2023-06-08 13:03:20,924] [INFO] Target genome list was writen to GCA_945877135.1_MiE-14oct19-235_genomic.fna/target_genomes.txt
[2023-06-08 13:03:20,928] [INFO] Task started: fastANI
[2023-06-08 13:03:20,929] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0350e2-1442-474c-8b40-86868384604a/GCA_945877135.1_MiE-14oct19-235_genomic.fna.gz --refList GCA_945877135.1_MiE-14oct19-235_genomic.fna/target_genomes.txt --output GCA_945877135.1_MiE-14oct19-235_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:03:39,728] [INFO] Task succeeded: fastANI
[2023-06-08 13:03:39,728] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:03:39,729] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:03:39,741] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:03:39,742] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 13:03:39,742] [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
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.3669	109	1197	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.2364	118	1197	95	below_threshold
Pirellulimonas nuda	strain=Pla175	GCA_007750855.1	2528009	2528009	type	True	76.1064	107	1197	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.092	120	1197	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	75.9691	58	1197	95	below_threshold
Pirellula staleyi	strain=DSM 6068	GCA_000025185.1	125	125	type	True	75.8895	51	1197	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.7069	78	1197	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.5681	62	1197	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.5668	62	1197	95	below_threshold
Lignipirellula cremea	strain=Pla85_3_4	GCA_007751035.1	2528010	2528010	type	True	75.1634	69	1197	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 13:03:39,744] [INFO] DFAST Taxonomy check result was written to GCA_945877135.1_MiE-14oct19-235_genomic.fna/tc_result.tsv
[2023-06-08 13:03:39,745] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:03:39,745] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:03:39,746] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/checkm_data
[2023-06-08 13:03:39,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:03:39,799] [INFO] Task started: CheckM
[2023-06-08 13:03:39,799] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945877135.1_MiE-14oct19-235_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945877135.1_MiE-14oct19-235_genomic.fna/checkm_input GCA_945877135.1_MiE-14oct19-235_genomic.fna/checkm_result
[2023-06-08 13:04:17,711] [INFO] Task succeeded: CheckM
[2023-06-08 13:04:17,712] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:04:17,732] [INFO] ===== Completeness check finished =====
[2023-06-08 13:04:17,732] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:04:17,733] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945877135.1_MiE-14oct19-235_genomic.fna/markers.fasta)
[2023-06-08 13:04:17,733] [INFO] Task started: Blastn
[2023-06-08 13:04:17,733] [INFO] Running command: blastn -query GCA_945877135.1_MiE-14oct19-235_genomic.fna/markers.fasta -db /var/lib/cwl/stg0307f5af-a11a-414c-a207-f9acdc8bdba1/dqc_reference/reference_markers_gtdb.fasta -out GCA_945877135.1_MiE-14oct19-235_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:04:18,637] [INFO] Task succeeded: Blastn
[2023-06-08 13:04:18,642] [INFO] Selected 16 target genomes.
[2023-06-08 13:04:18,642] [INFO] Target genome list was writen to GCA_945877135.1_MiE-14oct19-235_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:04:18,647] [INFO] Task started: fastANI
[2023-06-08 13:04:18,647] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0350e2-1442-474c-8b40-86868384604a/GCA_945877135.1_MiE-14oct19-235_genomic.fna.gz --refList GCA_945877135.1_MiE-14oct19-235_genomic.fna/target_genomes_gtdb.txt --output GCA_945877135.1_MiE-14oct19-235_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:04:28,389] [INFO] Task succeeded: fastANI
[2023-06-08 13:04:28,405] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 13:04:28,405] [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_018970605.1	s__QWPN01 sp018970605	79.0578	378	1197	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	79.0089	250	1197	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	78.9406	401	1197	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	78.9232	460	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	78.7806	404	1197	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	78.7141	368	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	78.6641	336	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_005789975.1	s__QWPN01 sp005789975	78.6194	324	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_016872925.1	s__QWPN01 sp016872925	78.6139	434	1197	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	78.5755	320	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	78.4243	372	1197	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	78.3854	365	1197	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	78.0709	349	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872555.1	s__F1-20-MAGs016 sp016872555	77.9593	392	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903949225.1	s__QWOP01 sp903949225	77.8343	303	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005791575.1	s__F1-20-MAGs016 sp005791575	77.687	338	1197	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:04:28,407] [INFO] GTDB search result was written to GCA_945877135.1_MiE-14oct19-235_genomic.fna/result_gtdb.tsv
[2023-06-08 13:04:28,408] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:04:28,412] [INFO] DFAST_QC result json was written to GCA_945877135.1_MiE-14oct19-235_genomic.fna/dqc_result.json
[2023-06-08 13:04:28,412] [INFO] DFAST_QC completed!
[2023-06-08 13:04:28,412] [INFO] Total running time: 0h1m21s