[2023-03-18 01:08:39,319] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:08:39,319] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:08:39,319] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference
[2023-03-18 01:08:40,421] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:08:40,421] [INFO] Task started: Prodigal
[2023-03-18 01:08:40,421] [INFO] Running command: cat /var/lib/cwl/stgcffe83cc-71cd-4a9d-a854-3d344ae7be16/OceanDNA-b506.fa | prodigal -d OceanDNA-b506/cds.fna -a OceanDNA-b506/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:08:54,841] [INFO] Task succeeded: Prodigal
[2023-03-18 01:08:54,841] [INFO] Task started: HMMsearch
[2023-03-18 01:08:54,841] [INFO] Running command: hmmsearch --tblout OceanDNA-b506/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/reference_markers.hmm OceanDNA-b506/protein.faa > /dev/null
[2023-03-18 01:08:55,009] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:08:55,009] [INFO] Found 6/6 markers.
[2023-03-18 01:08:55,032] [INFO] Query marker FASTA was written to OceanDNA-b506/markers.fasta
[2023-03-18 01:08:55,032] [INFO] Task started: Blastn
[2023-03-18 01:08:55,032] [INFO] Running command: blastn -query OceanDNA-b506/markers.fasta -db /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/reference_markers.fasta -out OceanDNA-b506/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:08:55,650] [INFO] Task succeeded: Blastn
[2023-03-18 01:08:55,655] [INFO] Selected 12 target genomes.
[2023-03-18 01:08:55,655] [INFO] Target genome list was writen to OceanDNA-b506/target_genomes.txt
[2023-03-18 01:08:55,665] [INFO] Task started: fastANI
[2023-03-18 01:08:55,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgcffe83cc-71cd-4a9d-a854-3d344ae7be16/OceanDNA-b506.fa --refList OceanDNA-b506/target_genomes.txt --output OceanDNA-b506/fastani_result.tsv --threads 1
[2023-03-18 01:09:04,981] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:04,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:09:04,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:09:04,987] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:09:04,987] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:09:04,987] [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	77.5012	291	767	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	77.0384	214	767	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	76.8237	193	767	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.4723	152	767	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	75.7723	83	767	95	below_threshold
Actinoplanes nipponensis	strain=NBRC 14063	GCA_016862275.1	135950	135950	type	True	75.0107	52	767	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:09:04,990] [INFO] DFAST Taxonomy check result was written to OceanDNA-b506/tc_result.tsv
[2023-03-18 01:09:04,990] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:09:04,990] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:09:04,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/checkm_data
[2023-03-18 01:09:04,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:09:04,999] [INFO] Task started: CheckM
[2023-03-18 01:09:05,000] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b506/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b506/checkm_input OceanDNA-b506/checkm_result
[2023-03-18 01:09:44,671] [INFO] Task succeeded: CheckM
[2023-03-18 01:09:44,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 01:09:44,761] [INFO] ===== Completeness check finished =====
[2023-03-18 01:09:44,761] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:09:44,761] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b506/markers.fasta)
[2023-03-18 01:09:44,761] [INFO] Task started: Blastn
[2023-03-18 01:09:44,761] [INFO] Running command: blastn -query OceanDNA-b506/markers.fasta -db /var/lib/cwl/stg6d03d800-d41d-4783-ad4a-78a0280465b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b506/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:09:45,658] [INFO] Task succeeded: Blastn
[2023-03-18 01:09:45,659] [INFO] Selected 11 target genomes.
[2023-03-18 01:09:45,659] [INFO] Target genome list was writen to OceanDNA-b506/target_genomes_gtdb.txt
[2023-03-18 01:09:45,669] [INFO] Task started: fastANI
[2023-03-18 01:09:45,670] [INFO] Running command: fastANI --query /var/lib/cwl/stgcffe83cc-71cd-4a9d-a854-3d344ae7be16/OceanDNA-b506.fa --refList OceanDNA-b506/target_genomes_gtdb.txt --output OceanDNA-b506/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:09:53,006] [INFO] Task succeeded: fastANI
[2023-03-18 01:09:53,013] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:09:53,013] [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	77.5115	290	767	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	77.2442	152	767	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_013213745.1	s__JABSQH01 sp013213745	77.0791	134	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__JABSQH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000350145.1	s__Ilumatobacter_A nonamiensis	77.0625	212	767	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	77.0328	181	767	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	76.8353	192	767	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	76.7279	126	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Ilumatobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426815.1	s__Desertimonas flava	76.5108	149	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__Desertimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_007122945.1	s__SKSP01 sp007122945	76.5073	126	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__Ilumatobacteraceae;g__SKSP01	95.0	99.05	99.05	0.83	0.83	2	-
GCF_009650215.1	s__Actinomarinicola tropica	75.7723	83	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826025.1	s__CADEDH01 sp902826025	75.4848	55	767	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SZUA-35;g__CADEDH01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:09:53,013] [INFO] GTDB search result was written to OceanDNA-b506/result_gtdb.tsv
[2023-03-18 01:09:53,013] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:09:53,015] [INFO] DFAST_QC result json was written to OceanDNA-b506/dqc_result.json
[2023-03-18 01:09:53,015] [INFO] DFAST_QC completed!
[2023-03-18 01:09:53,015] [INFO] Total running time: 0h1m14s