[2023-03-18 03:28:30,807] [INFO] DFAST_QC pipeline started.
[2023-03-18 03:28:30,807] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 03:28:30,807] [INFO] DQC Reference Directory: /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference
[2023-03-18 03:28:31,916] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 03:28:31,916] [INFO] Task started: Prodigal
[2023-03-18 03:28:31,916] [INFO] Running command: cat /var/lib/cwl/stgd8fa42b3-529c-4f0b-a971-6a50ca951651/OceanDNA-b484.fa | prodigal -d OceanDNA-b484/cds.fna -a OceanDNA-b484/protein.faa -g 11 -q > /dev/null
[2023-03-18 03:28:45,459] [INFO] Task succeeded: Prodigal
[2023-03-18 03:28:45,459] [INFO] Task started: HMMsearch
[2023-03-18 03:28:45,459] [INFO] Running command: hmmsearch --tblout OceanDNA-b484/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/reference_markers.hmm OceanDNA-b484/protein.faa > /dev/null
[2023-03-18 03:28:45,656] [INFO] Task succeeded: HMMsearch
[2023-03-18 03:28:45,656] [INFO] Found 6/6 markers.
[2023-03-18 03:28:45,672] [INFO] Query marker FASTA was written to OceanDNA-b484/markers.fasta
[2023-03-18 03:28:45,672] [INFO] Task started: Blastn
[2023-03-18 03:28:45,672] [INFO] Running command: blastn -query OceanDNA-b484/markers.fasta -db /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/reference_markers.fasta -out OceanDNA-b484/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:28:46,281] [INFO] Task succeeded: Blastn
[2023-03-18 03:28:46,282] [INFO] Selected 19 target genomes.
[2023-03-18 03:28:46,282] [INFO] Target genome list was writen to OceanDNA-b484/target_genomes.txt
[2023-03-18 03:28:46,292] [INFO] Task started: fastANI
[2023-03-18 03:28:46,292] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fa42b3-529c-4f0b-a971-6a50ca951651/OceanDNA-b484.fa --refList OceanDNA-b484/target_genomes.txt --output OceanDNA-b484/fastani_result.tsv --threads 1
[2023-03-18 03:29:00,209] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:00,209] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 03:29:00,209] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 03:29:00,214] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 03:29:00,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 03:29:00,214] [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 coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.8839	266	699	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.4845	163	699	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.7804	143	699	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.5266	122	699	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.7386	50	699	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 03:29:00,214] [INFO] DFAST Taxonomy check result was written to OceanDNA-b484/tc_result.tsv
[2023-03-18 03:29:00,214] [INFO] ===== Taxonomy check completed =====
[2023-03-18 03:29:00,214] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 03:29:00,214] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/checkm_data
[2023-03-18 03:29:00,215] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 03:29:00,219] [INFO] Task started: CheckM
[2023-03-18 03:29:00,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b484/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b484/checkm_input OceanDNA-b484/checkm_result
[2023-03-18 03:29:37,433] [INFO] Task succeeded: CheckM
[2023-03-18 03:29:37,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 03:29:37,435] [INFO] ===== Completeness check finished =====
[2023-03-18 03:29:37,435] [INFO] ===== Start GTDB Search =====
[2023-03-18 03:29:37,435] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b484/markers.fasta)
[2023-03-18 03:29:37,436] [INFO] Task started: Blastn
[2023-03-18 03:29:37,436] [INFO] Running command: blastn -query OceanDNA-b484/markers.fasta -db /var/lib/cwl/stg6584c1dd-1bcb-4863-83f4-3a18dd78c555/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b484/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 03:29:38,506] [INFO] Task succeeded: Blastn
[2023-03-18 03:29:38,507] [INFO] Selected 20 target genomes.
[2023-03-18 03:29:38,507] [INFO] Target genome list was writen to OceanDNA-b484/target_genomes_gtdb.txt
[2023-03-18 03:29:38,524] [INFO] Task started: fastANI
[2023-03-18 03:29:38,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgd8fa42b3-529c-4f0b-a971-6a50ca951651/OceanDNA-b484.fa --refList OceanDNA-b484/target_genomes_gtdb.txt --output OceanDNA-b484/fastani_result_gtdb.tsv --threads 1
[2023-03-18 03:29:49,346] [INFO] Task succeeded: fastANI
[2023-03-18 03:29:49,353] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 03:29:49,354] [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_905182555.1	s__Ilumatobacter_A sp905182555	85.8023	474	699	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	78.5627	273	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.79	99.78	0.94	0.93	4	-
GCF_000348785.1	s__Ilumatobacter_A coccineus	77.8963	265	699	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_000350145.1	s__Ilumatobacter_A nonamiensis	77.4845	163	699	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_013002175.1	s__Ilumatobacter_A sp013002175	77.2627	223	699	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_002711735.1	s__Ilumatobacter_A sp002711735	77.2394	118	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.50	99.50	0.82	0.82	2	-
GCF_004364865.1	s__Ilumatobacter fluminis	76.7958	142	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009704985.1	s__VFMC01 sp009704985	76.7773	107	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480335.1	s__Ilumatobacter_A sp905480335	76.6678	107	699	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_013213745.1	s__JABSQH01 sp013213745	76.629	118	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	76.4851	113	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016700055.1	s__Kalu-18 sp016700055	76.2087	69	699	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Kalu-18	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 03:29:49,354] [INFO] GTDB search result was written to OceanDNA-b484/result_gtdb.tsv
[2023-03-18 03:29:49,354] [INFO] ===== GTDB Search completed =====
[2023-03-18 03:29:49,355] [INFO] DFAST_QC result json was written to OceanDNA-b484/dqc_result.json
[2023-03-18 03:29:49,355] [INFO] DFAST_QC completed!
[2023-03-18 03:29:49,355] [INFO] Total running time: 0h1m19s