[2023-03-18 08:55:50,645] [INFO] DFAST_QC pipeline started.
[2023-03-18 08:55:50,646] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 08:55:50,646] [INFO] DQC Reference Directory: /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference
[2023-03-18 08:55:51,858] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 08:55:51,859] [INFO] Task started: Prodigal
[2023-03-18 08:55:51,859] [INFO] Running command: cat /var/lib/cwl/stg55546efe-b003-410a-9157-c28fe04b04c6/OceanDNA-b500.fa | prodigal -d OceanDNA-b500/cds.fna -a OceanDNA-b500/protein.faa -g 11 -q > /dev/null
[2023-03-18 08:56:05,537] [INFO] Task succeeded: Prodigal
[2023-03-18 08:56:05,537] [INFO] Task started: HMMsearch
[2023-03-18 08:56:05,537] [INFO] Running command: hmmsearch --tblout OceanDNA-b500/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/reference_markers.hmm OceanDNA-b500/protein.faa > /dev/null
[2023-03-18 08:56:05,695] [INFO] Task succeeded: HMMsearch
[2023-03-18 08:56:05,696] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg55546efe-b003-410a-9157-c28fe04b04c6/OceanDNA-b500.fa]
[2023-03-18 08:56:05,714] [INFO] Query marker FASTA was written to OceanDNA-b500/markers.fasta
[2023-03-18 08:56:05,715] [INFO] Task started: Blastn
[2023-03-18 08:56:05,715] [INFO] Running command: blastn -query OceanDNA-b500/markers.fasta -db /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/reference_markers.fasta -out OceanDNA-b500/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:56:06,226] [INFO] Task succeeded: Blastn
[2023-03-18 08:56:06,227] [INFO] Selected 9 target genomes.
[2023-03-18 08:56:06,227] [INFO] Target genome list was writen to OceanDNA-b500/target_genomes.txt
[2023-03-18 08:56:06,233] [INFO] Task started: fastANI
[2023-03-18 08:56:06,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg55546efe-b003-410a-9157-c28fe04b04c6/OceanDNA-b500.fa --refList OceanDNA-b500/target_genomes.txt --output OceanDNA-b500/fastani_result.tsv --threads 1
[2023-03-18 08:56:13,852] [INFO] Task succeeded: fastANI
[2023-03-18 08:56:13,852] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 08:56:13,852] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 08:56:13,858] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 08:56:13,858] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 08:56:13,858] [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	79.5146	427	754	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	78.694	316	754	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	77.1463	250	754	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.3917	216	754	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	75.6987	98	754	95	below_threshold
Kitasatospora herbaricolor	strain=JCM 4138	GCA_014648975.1	68217	68217	type	True	74.8377	88	754	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 08:56:13,858] [INFO] DFAST Taxonomy check result was written to OceanDNA-b500/tc_result.tsv
[2023-03-18 08:56:13,858] [INFO] ===== Taxonomy check completed =====
[2023-03-18 08:56:13,858] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 08:56:13,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/checkm_data
[2023-03-18 08:56:13,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 08:56:13,867] [INFO] Task started: CheckM
[2023-03-18 08:56:13,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b500/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b500/checkm_input OceanDNA-b500/checkm_result
[2023-03-18 08:57:00,252] [INFO] Task succeeded: CheckM
[2023-03-18 08:57:00,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 08:57:00,257] [INFO] ===== Completeness check finished =====
[2023-03-18 08:57:00,257] [INFO] ===== Start GTDB Search =====
[2023-03-18 08:57:00,257] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b500/markers.fasta)
[2023-03-18 08:57:00,258] [INFO] Task started: Blastn
[2023-03-18 08:57:00,258] [INFO] Running command: blastn -query OceanDNA-b500/markers.fasta -db /var/lib/cwl/stgff64b04d-3849-4fd3-bca8-9348c3188f46/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b500/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 08:57:00,943] [INFO] Task succeeded: Blastn
[2023-03-18 08:57:00,944] [INFO] Selected 9 target genomes.
[2023-03-18 08:57:00,944] [INFO] Target genome list was writen to OceanDNA-b500/target_genomes_gtdb.txt
[2023-03-18 08:57:00,953] [INFO] Task started: fastANI
[2023-03-18 08:57:00,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg55546efe-b003-410a-9157-c28fe04b04c6/OceanDNA-b500.fa --refList OceanDNA-b500/target_genomes_gtdb.txt --output OceanDNA-b500/fastani_result_gtdb.tsv --threads 1
[2023-03-18 08:57:07,136] [INFO] Task succeeded: fastANI
[2023-03-18 08:57:07,142] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 08:57:07,142] [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
GCF_000348785.1	s__Ilumatobacter_A coccineus	79.5506	424	754	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	78.6937	317	754	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	77.8255	260	754	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	77.1463	250	754	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018666235.1	s__Ilumatobacter_A sp018666235	77.09	141	754	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	77.0814	193	754	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007122945.1	s__SKSP01 sp007122945	76.8099	212	754	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCA_015767405.1	s__Sva-07 sp015767405	76.5452	83	754	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Sva-07	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 08:57:07,142] [INFO] GTDB search result was written to OceanDNA-b500/result_gtdb.tsv
[2023-03-18 08:57:07,142] [INFO] ===== GTDB Search completed =====
[2023-03-18 08:57:07,143] [INFO] DFAST_QC result json was written to OceanDNA-b500/dqc_result.json
[2023-03-18 08:57:07,143] [INFO] DFAST_QC completed!
[2023-03-18 08:57:07,143] [INFO] Total running time: 0h1m16s