[2023-03-17 07:01:49,039] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:01:49,039] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:01:49,039] [INFO] DQC Reference Directory: /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference
[2023-03-17 07:01:50,166] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:01:50,167] [INFO] Task started: Prodigal
[2023-03-17 07:01:50,167] [INFO] Running command: cat /var/lib/cwl/stgfde54115-d102-4bf6-92f5-a40cb3050794/OceanDNA-b517.fa | prodigal -d OceanDNA-b517/cds.fna -a OceanDNA-b517/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:02:07,780] [INFO] Task succeeded: Prodigal
[2023-03-17 07:02:07,780] [INFO] Task started: HMMsearch
[2023-03-17 07:02:07,780] [INFO] Running command: hmmsearch --tblout OceanDNA-b517/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/reference_markers.hmm OceanDNA-b517/protein.faa > /dev/null
[2023-03-17 07:02:07,983] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:02:07,984] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfde54115-d102-4bf6-92f5-a40cb3050794/OceanDNA-b517.fa]
[2023-03-17 07:02:08,009] [INFO] Query marker FASTA was written to OceanDNA-b517/markers.fasta
[2023-03-17 07:02:08,010] [INFO] Task started: Blastn
[2023-03-17 07:02:08,010] [INFO] Running command: blastn -query OceanDNA-b517/markers.fasta -db /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/reference_markers.fasta -out OceanDNA-b517/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:02:08,767] [INFO] Task succeeded: Blastn
[2023-03-17 07:02:08,768] [INFO] Selected 10 target genomes.
[2023-03-17 07:02:08,768] [INFO] Target genome list was writen to OceanDNA-b517/target_genomes.txt
[2023-03-17 07:02:08,774] [INFO] Task started: fastANI
[2023-03-17 07:02:08,774] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde54115-d102-4bf6-92f5-a40cb3050794/OceanDNA-b517.fa --refList OceanDNA-b517/target_genomes.txt --output OceanDNA-b517/fastani_result.tsv --threads 1
[2023-03-17 07:02:15,826] [INFO] Task succeeded: fastANI
[2023-03-17 07:02:15,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:02:15,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:02:15,833] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:02:15,833] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:02:15,833] [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 fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	78.8411	383	880	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.4827	223	880	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	77.3979	260	880	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	77.0309	267	880	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.1961	149	880	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.732	134	880	95	below_threshold
Nocardioides seonyuensis	strain=MMS17-SY207-3	GCA_004683965.1	2518371	2518371	type	True	75.1867	68	880	95	below_threshold
Nocardioides currus	strain=IB-3	GCA_003057875.1	2133958	2133958	type	True	74.9229	108	880	95	below_threshold
Actinomycetospora chiangmaiensis	strain=DSM 45062	GCA_000379625.1	402650	402650	type	True	74.8065	123	880	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:02:15,833] [INFO] DFAST Taxonomy check result was written to OceanDNA-b517/tc_result.tsv
[2023-03-17 07:02:15,833] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:02:15,833] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:02:15,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/checkm_data
[2023-03-17 07:02:15,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:02:15,839] [INFO] Task started: CheckM
[2023-03-17 07:02:15,839] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b517/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b517/checkm_input OceanDNA-b517/checkm_result
[2023-03-17 07:03:01,325] [INFO] Task succeeded: CheckM
[2023-03-17 07:03:01,325] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-17 07:03:01,328] [INFO] ===== Completeness check finished =====
[2023-03-17 07:03:01,328] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:03:01,328] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b517/markers.fasta)
[2023-03-17 07:03:01,329] [INFO] Task started: Blastn
[2023-03-17 07:03:01,329] [INFO] Running command: blastn -query OceanDNA-b517/markers.fasta -db /var/lib/cwl/stg20618c6b-d14a-4325-a29c-5fc6ff80ae9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b517/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:03:02,482] [INFO] Task succeeded: Blastn
[2023-03-17 07:03:02,482] [INFO] Selected 11 target genomes.
[2023-03-17 07:03:02,482] [INFO] Target genome list was writen to OceanDNA-b517/target_genomes_gtdb.txt
[2023-03-17 07:03:02,724] [INFO] Task started: fastANI
[2023-03-17 07:03:02,724] [INFO] Running command: fastANI --query /var/lib/cwl/stgfde54115-d102-4bf6-92f5-a40cb3050794/OceanDNA-b517.fa --refList OceanDNA-b517/target_genomes_gtdb.txt --output OceanDNA-b517/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:03:10,127] [INFO] Task succeeded: fastANI
[2023-03-17 07:03:10,134] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:03:10,134] [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_002698945.1	s__Ilumatobacter sp002698945	79.3788	350	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364865.1	s__Ilumatobacter fluminis	78.8404	383	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002175.1	s__Ilumatobacter_A sp013002175	77.7876	241	880	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_007693335.1	s__SKSP01 sp007693335	77.7557	232	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	77.6988	246	880	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	77.4836	223	880	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	77.3856	261	880	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_010024485.1	s__Casp-actino5 sp010024485	77.3831	87	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Casp-actino5	95.0	98.53	98.53	0.77	0.77	2	-
GCA_009704985.1	s__VFMC01 sp009704985	77.1032	237	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__VFMC01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	77.0503	264	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.7015	153	880	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:03:10,134] [INFO] GTDB search result was written to OceanDNA-b517/result_gtdb.tsv
[2023-03-17 07:03:10,134] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:03:10,136] [INFO] DFAST_QC result json was written to OceanDNA-b517/dqc_result.json
[2023-03-17 07:03:10,136] [INFO] DFAST_QC completed!
[2023-03-17 07:03:10,136] [INFO] Total running time: 0h1m21s