[2023-03-16 18:04:18,918] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:04:18,918] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:04:18,918] [INFO] DQC Reference Directory: /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference
[2023-03-16 18:04:20,202] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:04:20,203] [INFO] Task started: Prodigal
[2023-03-16 18:04:20,203] [INFO] Running command: cat /var/lib/cwl/stgcd31c952-2142-4e4d-8826-81fc9f783231/OceanDNA-b466.fa | prodigal -d OceanDNA-b466/cds.fna -a OceanDNA-b466/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:04:52,885] [INFO] Task succeeded: Prodigal
[2023-03-16 18:04:52,886] [INFO] Task started: HMMsearch
[2023-03-16 18:04:52,886] [INFO] Running command: hmmsearch --tblout OceanDNA-b466/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/reference_markers.hmm OceanDNA-b466/protein.faa > /dev/null
[2023-03-16 18:04:53,127] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:04:53,128] [INFO] Found 6/6 markers.
[2023-03-16 18:04:53,151] [INFO] Query marker FASTA was written to OceanDNA-b466/markers.fasta
[2023-03-16 18:04:53,154] [INFO] Task started: Blastn
[2023-03-16 18:04:53,154] [INFO] Running command: blastn -query OceanDNA-b466/markers.fasta -db /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/reference_markers.fasta -out OceanDNA-b466/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:04:53,969] [INFO] Task succeeded: Blastn
[2023-03-16 18:04:53,970] [INFO] Selected 19 target genomes.
[2023-03-16 18:04:53,970] [INFO] Target genome list was writen to OceanDNA-b466/target_genomes.txt
[2023-03-16 18:04:53,984] [INFO] Task started: fastANI
[2023-03-16 18:04:53,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd31c952-2142-4e4d-8826-81fc9f783231/OceanDNA-b466.fa --refList OceanDNA-b466/target_genomes.txt --output OceanDNA-b466/fastani_result.tsv --threads 1
[2023-03-16 18:05:11,440] [INFO] Task succeeded: fastANI
[2023-03-16 18:05:11,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:05:11,440] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:05:11,497] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:05:11,497] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:05:11,497] [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	77.3005	316	1070	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.7615	234	1070	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.2966	153	1070	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0756	126	1070	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	74.8433	66	1070	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:05:11,497] [INFO] DFAST Taxonomy check result was written to OceanDNA-b466/tc_result.tsv
[2023-03-16 18:05:11,498] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:05:11,498] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:05:11,498] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/checkm_data
[2023-03-16 18:05:11,499] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:05:11,504] [INFO] Task started: CheckM
[2023-03-16 18:05:11,504] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b466/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b466/checkm_input OceanDNA-b466/checkm_result
[2023-03-16 18:06:16,811] [INFO] Task succeeded: CheckM
[2023-03-16 18:06:16,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:06:16,814] [INFO] ===== Completeness check finished =====
[2023-03-16 18:06:16,814] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:06:16,814] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b466/markers.fasta)
[2023-03-16 18:06:16,815] [INFO] Task started: Blastn
[2023-03-16 18:06:16,815] [INFO] Running command: blastn -query OceanDNA-b466/markers.fasta -db /var/lib/cwl/stg182e04ed-fb64-4356-b446-2f9bb9e5ebc6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b466/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:06:18,260] [INFO] Task succeeded: Blastn
[2023-03-16 18:06:18,261] [INFO] Selected 20 target genomes.
[2023-03-16 18:06:18,261] [INFO] Target genome list was writen to OceanDNA-b466/target_genomes_gtdb.txt
[2023-03-16 18:06:18,276] [INFO] Task started: fastANI
[2023-03-16 18:06:18,276] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd31c952-2142-4e4d-8826-81fc9f783231/OceanDNA-b466.fa --refList OceanDNA-b466/target_genomes_gtdb.txt --output OceanDNA-b466/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:06:29,118] [INFO] Task succeeded: fastANI
[2023-03-16 18:06:29,124] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:06:29,125] [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	90.387	615	1070	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	77.8176	346	1070	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	77.3094	315	1070	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	77.279	255	1070	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	76.7712	233	1070	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	76.7013	117	1070	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter_A	95.0	99.50	99.50	0.82	0.82	2	-
GCA_905480335.1	s__Ilumatobacter_A sp905480335	76.4727	121	1070	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	76.3075	152	1070	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698945.1	s__Ilumatobacter sp002698945	76.1533	132	1070	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013213745.1	s__JABSQH01 sp013213745	76.0755	124	1070	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:06:29,125] [INFO] GTDB search result was written to OceanDNA-b466/result_gtdb.tsv
[2023-03-16 18:06:29,125] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:06:29,126] [INFO] DFAST_QC result json was written to OceanDNA-b466/dqc_result.json
[2023-03-16 18:06:29,126] [INFO] DFAST_QC completed!
[2023-03-16 18:06:29,126] [INFO] Total running time: 0h2m10s