[2023-03-15 22:23:01,926] [INFO] DFAST_QC pipeline started.
[2023-03-15 22:23:01,926] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 22:23:01,926] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference
[2023-03-15 22:23:03,673] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 22:23:03,673] [INFO] Task started: Prodigal
[2023-03-15 22:23:03,673] [INFO] Running command: cat /var/lib/cwl/stgcba8ecdd-bd98-424e-a1d9-b352e584b626/OceanDNA-b328.fa | prodigal -d OceanDNA-b328/cds.fna -a OceanDNA-b328/protein.faa -g 11 -q > /dev/null
[2023-03-15 22:23:11,718] [INFO] Task succeeded: Prodigal
[2023-03-15 22:23:11,718] [INFO] Task started: HMMsearch
[2023-03-15 22:23:11,719] [INFO] Running command: hmmsearch --tblout OceanDNA-b328/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/reference_markers.hmm OceanDNA-b328/protein.faa > /dev/null
[2023-03-15 22:23:11,879] [INFO] Task succeeded: HMMsearch
[2023-03-15 22:23:11,879] [INFO] Found 6/6 markers.
[2023-03-15 22:23:11,896] [INFO] Query marker FASTA was written to OceanDNA-b328/markers.fasta
[2023-03-15 22:23:11,896] [INFO] Task started: Blastn
[2023-03-15 22:23:11,896] [INFO] Running command: blastn -query OceanDNA-b328/markers.fasta -db /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/reference_markers.fasta -out OceanDNA-b328/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:12,567] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:12,568] [INFO] Selected 15 target genomes.
[2023-03-15 22:23:12,568] [INFO] Target genome list was writen to OceanDNA-b328/target_genomes.txt
[2023-03-15 22:23:12,578] [INFO] Task started: fastANI
[2023-03-15 22:23:12,578] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba8ecdd-bd98-424e-a1d9-b352e584b626/OceanDNA-b328.fa --refList OceanDNA-b328/target_genomes.txt --output OceanDNA-b328/fastani_result.tsv --threads 1
[2023-03-15 22:23:22,166] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:22,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 22:23:22,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 22:23:22,171] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 22:23:22,171] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 22:23:22,172] [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
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.7028	91	265	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.652	98	265	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.5213	79	265	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.4268	81	265	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.3223	54	265	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 22:23:22,172] [INFO] DFAST Taxonomy check result was written to OceanDNA-b328/tc_result.tsv
[2023-03-15 22:23:22,172] [INFO] ===== Taxonomy check completed =====
[2023-03-15 22:23:22,172] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 22:23:22,172] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/checkm_data
[2023-03-15 22:23:22,173] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 22:23:22,299] [INFO] Task started: CheckM
[2023-03-15 22:23:22,300] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b328/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b328/checkm_input OceanDNA-b328/checkm_result
[2023-03-15 22:23:47,261] [INFO] Task succeeded: CheckM
[2023-03-15 22:23:47,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.60%
Contamintation: 1.36%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 22:23:47,263] [INFO] ===== Completeness check finished =====
[2023-03-15 22:23:47,264] [INFO] ===== Start GTDB Search =====
[2023-03-15 22:23:47,264] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b328/markers.fasta)
[2023-03-15 22:23:47,264] [INFO] Task started: Blastn
[2023-03-15 22:23:47,264] [INFO] Running command: blastn -query OceanDNA-b328/markers.fasta -db /var/lib/cwl/stgbe62035a-2e7d-44b1-8242-abfff8380f73/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b328/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 22:23:48,284] [INFO] Task succeeded: Blastn
[2023-03-15 22:23:48,285] [INFO] Selected 15 target genomes.
[2023-03-15 22:23:48,285] [INFO] Target genome list was writen to OceanDNA-b328/target_genomes_gtdb.txt
[2023-03-15 22:23:48,297] [INFO] Task started: fastANI
[2023-03-15 22:23:48,297] [INFO] Running command: fastANI --query /var/lib/cwl/stgcba8ecdd-bd98-424e-a1d9-b352e584b626/OceanDNA-b328.fa --refList OceanDNA-b328/target_genomes_gtdb.txt --output OceanDNA-b328/fastani_result_gtdb.tsv --threads 1
[2023-03-15 22:23:56,683] [INFO] Task succeeded: fastANI
[2023-03-15 22:23:56,690] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 22:23:56,690] [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_013213745.1	s__JABSQH01 sp013213745	99.6135	263	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_013811855.1	s__JACCUL01 sp013811855	77.7621	56	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JACCUL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.7402	78	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.7028	91	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.652	98	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	77.5601	78	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007693335.1	s__SKSP01 sp007693335	77.4481	81	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	77.4268	81	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.3889	107	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	77.1842	65	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCA_002698945.1	s__Ilumatobacter sp002698945	77.0605	66	265	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 22:23:56,691] [INFO] GTDB search result was written to OceanDNA-b328/result_gtdb.tsv
[2023-03-15 22:23:56,691] [INFO] ===== GTDB Search completed =====
[2023-03-15 22:23:56,692] [INFO] DFAST_QC result json was written to OceanDNA-b328/dqc_result.json
[2023-03-15 22:23:56,692] [INFO] DFAST_QC completed!
[2023-03-15 22:23:56,692] [INFO] Total running time: 0h0m55s