[2023-06-19 02:46:01,611] [INFO] DFAST_QC pipeline started.
[2023-06-19 02:46:01,613] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 02:46:01,613] [INFO] DQC Reference Directory: /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference
[2023-06-19 02:46:03,410] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 02:46:03,411] [INFO] Task started: Prodigal
[2023-06-19 02:46:03,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg532e2c42-e19b-4360-af95-d38348488f4a/GCA_013042435.1_ASM1304243v1_genomic.fna.gz | prodigal -d GCA_013042435.1_ASM1304243v1_genomic.fna/cds.fna -a GCA_013042435.1_ASM1304243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 02:46:15,464] [INFO] Task succeeded: Prodigal
[2023-06-19 02:46:15,465] [INFO] Task started: HMMsearch
[2023-06-19 02:46:15,465] [INFO] Running command: hmmsearch --tblout GCA_013042435.1_ASM1304243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/reference_markers.hmm GCA_013042435.1_ASM1304243v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 02:46:15,755] [INFO] Task succeeded: HMMsearch
[2023-06-19 02:46:15,757] [INFO] Found 6/6 markers.
[2023-06-19 02:46:15,804] [INFO] Query marker FASTA was written to GCA_013042435.1_ASM1304243v1_genomic.fna/markers.fasta
[2023-06-19 02:46:15,804] [INFO] Task started: Blastn
[2023-06-19 02:46:15,804] [INFO] Running command: blastn -query GCA_013042435.1_ASM1304243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/reference_markers.fasta -out GCA_013042435.1_ASM1304243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:46:16,445] [INFO] Task succeeded: Blastn
[2023-06-19 02:46:16,449] [INFO] Selected 32 target genomes.
[2023-06-19 02:46:16,450] [INFO] Target genome list was writen to GCA_013042435.1_ASM1304243v1_genomic.fna/target_genomes.txt
[2023-06-19 02:46:16,453] [INFO] Task started: fastANI
[2023-06-19 02:46:16,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg532e2c42-e19b-4360-af95-d38348488f4a/GCA_013042435.1_ASM1304243v1_genomic.fna.gz --refList GCA_013042435.1_ASM1304243v1_genomic.fna/target_genomes.txt --output GCA_013042435.1_ASM1304243v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 02:46:40,283] [INFO] Task succeeded: fastANI
[2023-06-19 02:46:40,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 02:46:40,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 02:46:40,296] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 02:46:40,296] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 02:46:40,296] [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
Sandaracinus amylolyticus	strain=DSM 53668	GCA_000737325.2	927083	927083	type	True	75.4982	162	1371	95	below_threshold
Labilithrix luteola	strain=DSM 27648	GCA_001263205.1	1391654	1391654	type	True	75.2344	89	1371	95	below_threshold
Polyangium spumosum	strain=DSM 14734	GCA_009649845.1	889282	889282	type	True	75.1736	114	1371	95	below_threshold
Polyangium fumosum	strain=DSM 14668	GCA_005144585.1	889272	889272	neotype	True	75.1663	105	1371	95	below_threshold
Polyangium aurulentum	strain=SDU3-1	GCA_005144635.2	2567896	2567896	type	True	75.1553	135	1371	95	below_threshold
Glycomyces sambucus	strain=CGMCC 4.3147	GCA_900102815.1	380244	380244	type	True	74.7927	50	1371	95	below_threshold
Burkholderia arboris		GCA_902499125.1	488730	488730	type	True	74.77	62	1371	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 02:46:40,298] [INFO] DFAST Taxonomy check result was written to GCA_013042435.1_ASM1304243v1_genomic.fna/tc_result.tsv
[2023-06-19 02:46:40,299] [INFO] ===== Taxonomy check completed =====
[2023-06-19 02:46:40,299] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 02:46:40,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/checkm_data
[2023-06-19 02:46:40,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 02:46:40,345] [INFO] Task started: CheckM
[2023-06-19 02:46:40,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013042435.1_ASM1304243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013042435.1_ASM1304243v1_genomic.fna/checkm_input GCA_013042435.1_ASM1304243v1_genomic.fna/checkm_result
[2023-06-19 02:47:18,713] [INFO] Task succeeded: CheckM
[2023-06-19 02:47:18,714] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 02:47:18,738] [INFO] ===== Completeness check finished =====
[2023-06-19 02:47:18,739] [INFO] ===== Start GTDB Search =====
[2023-06-19 02:47:18,739] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013042435.1_ASM1304243v1_genomic.fna/markers.fasta)
[2023-06-19 02:47:18,739] [INFO] Task started: Blastn
[2023-06-19 02:47:18,740] [INFO] Running command: blastn -query GCA_013042435.1_ASM1304243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg246f9178-ab85-43c6-aebb-7288f76dfca8/dqc_reference/reference_markers_gtdb.fasta -out GCA_013042435.1_ASM1304243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 02:47:19,665] [INFO] Task succeeded: Blastn
[2023-06-19 02:47:19,669] [INFO] Selected 12 target genomes.
[2023-06-19 02:47:19,670] [INFO] Target genome list was writen to GCA_013042435.1_ASM1304243v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 02:47:19,673] [INFO] Task started: fastANI
[2023-06-19 02:47:19,673] [INFO] Running command: fastANI --query /var/lib/cwl/stg532e2c42-e19b-4360-af95-d38348488f4a/GCA_013042435.1_ASM1304243v1_genomic.fna.gz --refList GCA_013042435.1_ASM1304243v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013042435.1_ASM1304243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 02:47:33,101] [INFO] Task succeeded: fastANI
[2023-06-19 02:47:33,123] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 02:47:33,124] [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_004283055.1	s__SG8-38 sp004283055	99.7094	1217	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	99.78	99.72	0.93	0.90	8	conclusive
GCA_013002645.1	s__SG8-38 sp013002645	82.5192	688	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003647035.1	s__SG8-38 sp003647035	78.4192	432	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	96.70	96.70	0.74	0.74	2	-
GCA_001303415.1	s__SG8-38 sp001303415	77.7491	395	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__SG8-38	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017644045.1	s__UBA1660 sp017644045	76.2185	148	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002699025.1	s__GCA-2699025 sp002699025	76.1288	190	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__GCA-2699025	95.0	99.90	99.85	0.97	0.97	3	-
GCA_012744445.1	s__JAAYBZ01 sp012744445	76.0888	139	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__JAAYBZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002320815.1	s__UBA1660 sp002320815	75.8228	133	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Polyangiales;f__SG8-38;g__UBA1660	95.0	99.96	99.96	0.96	0.96	2	-
GCA_016793465.1	s__Nannocystis sp016793465	74.9217	99	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812955.1	s__Nannocystis sp013812955	74.888	61	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Nannocystis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013812655.1	s__JABFXX01 sp013812655	74.8525	80	1371	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__JABFXX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 02:47:33,126] [INFO] GTDB search result was written to GCA_013042435.1_ASM1304243v1_genomic.fna/result_gtdb.tsv
[2023-06-19 02:47:33,127] [INFO] ===== GTDB Search completed =====
[2023-06-19 02:47:33,130] [INFO] DFAST_QC result json was written to GCA_013042435.1_ASM1304243v1_genomic.fna/dqc_result.json
[2023-06-19 02:47:33,130] [INFO] DFAST_QC completed!
[2023-06-19 02:47:33,130] [INFO] Total running time: 0h1m32s