[2023-03-17 07:44:36,993] [INFO] DFAST_QC pipeline started.
[2023-03-17 07:44:36,993] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 07:44:36,993] [INFO] DQC Reference Directory: /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference
[2023-03-17 07:44:38,856] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 07:44:38,856] [INFO] Task started: Prodigal
[2023-03-17 07:44:38,856] [INFO] Running command: cat /var/lib/cwl/stg353d2aba-4f9d-477a-b4d8-97e71cc8fd9c/OceanDNA-b3314.fa | prodigal -d OceanDNA-b3314/cds.fna -a OceanDNA-b3314/protein.faa -g 11 -q > /dev/null
[2023-03-17 07:44:46,778] [INFO] Task succeeded: Prodigal
[2023-03-17 07:44:46,778] [INFO] Task started: HMMsearch
[2023-03-17 07:44:46,778] [INFO] Running command: hmmsearch --tblout OceanDNA-b3314/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/reference_markers.hmm OceanDNA-b3314/protein.faa > /dev/null
[2023-03-17 07:44:46,947] [INFO] Task succeeded: HMMsearch
[2023-03-17 07:44:46,947] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg353d2aba-4f9d-477a-b4d8-97e71cc8fd9c/OceanDNA-b3314.fa]
[2023-03-17 07:44:46,966] [INFO] Query marker FASTA was written to OceanDNA-b3314/markers.fasta
[2023-03-17 07:44:46,966] [INFO] Task started: Blastn
[2023-03-17 07:44:46,966] [INFO] Running command: blastn -query OceanDNA-b3314/markers.fasta -db /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/reference_markers.fasta -out OceanDNA-b3314/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:44:47,646] [INFO] Task succeeded: Blastn
[2023-03-17 07:44:47,647] [INFO] Selected 12 target genomes.
[2023-03-17 07:44:47,648] [INFO] Target genome list was writen to OceanDNA-b3314/target_genomes.txt
[2023-03-17 07:44:47,653] [INFO] Task started: fastANI
[2023-03-17 07:44:47,653] [INFO] Running command: fastANI --query /var/lib/cwl/stg353d2aba-4f9d-477a-b4d8-97e71cc8fd9c/OceanDNA-b3314.fa --refList OceanDNA-b3314/target_genomes.txt --output OceanDNA-b3314/fastani_result.tsv --threads 1
[2023-03-17 07:44:55,599] [INFO] Task succeeded: fastANI
[2023-03-17 07:44:55,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 07:44:55,600] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 07:44:55,608] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 07:44:55,608] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 07:44:55,608] [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
Nocardioides okcheonensis	strain=MMS20-HV4-12	GCA_020991065.1	2894081	2894081	type	True	84.8329	204	240	95	below_threshold
Nocardioides lacusdianchii	strain=JXJ CY 38	GCA_020102855.1	2783664	2783664	type	True	84.4965	197	240	95	below_threshold
Nocardioides furvisabuli	strain=JCM 13813	GCA_021083185.1	375542	375542	type	True	84.495	195	240	95	below_threshold
Nocardioides exalbidus	strain=DSM 22017	GCA_900105585.1	402596	402596	type	True	84.4793	214	240	95	below_threshold
Nocardioides cavernae	strain=DSM 29950	GCA_016907475.1	1921566	1921566	type	True	84.3859	203	240	95	below_threshold
Nocardioides cavernae	strain=KCTC 39551	GCA_014779675.1	1921566	1921566	type	True	84.3125	203	240	95	below_threshold
Nocardioides glacieisoli	strain=HLT3-15	GCA_004137245.1	1168730	1168730	type	True	84.2385	194	240	95	below_threshold
Nocardioides hwasunensis	strain=19197	GCA_014779665.1	397258	397258	type	True	84.1456	210	240	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	84.0698	197	240	95	below_threshold
Nocardioides alpinus	strain=CGMCC 1.10697	GCA_900112035.1	748909	748909	type	True	83.9655	198	240	95	below_threshold
Nocardioides alpinus	strain=DSM 23325	GCA_002836395.1	748909	748909	type	True	83.9063	199	240	95	below_threshold
Nocardioides astragali	strain=CGMCC 4.7327	GCA_024436375.1	1776736	1776736	type	True	83.8025	190	240	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 07:44:55,608] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3314/tc_result.tsv
[2023-03-17 07:44:55,609] [INFO] ===== Taxonomy check completed =====
[2023-03-17 07:44:55,609] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 07:44:55,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/checkm_data
[2023-03-17 07:44:55,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 07:44:55,614] [INFO] Task started: CheckM
[2023-03-17 07:44:55,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3314/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3314/checkm_input OceanDNA-b3314/checkm_result
[2023-03-17 07:45:20,289] [INFO] Task succeeded: CheckM
[2023-03-17 07:45:20,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.75%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-17 07:45:20,292] [INFO] ===== Completeness check finished =====
[2023-03-17 07:45:20,292] [INFO] ===== Start GTDB Search =====
[2023-03-17 07:45:20,292] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3314/markers.fasta)
[2023-03-17 07:45:20,293] [INFO] Task started: Blastn
[2023-03-17 07:45:20,293] [INFO] Running command: blastn -query OceanDNA-b3314/markers.fasta -db /var/lib/cwl/stgeadbbdd6-85d0-4f3a-a4a3-0028a01d7362/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3314/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 07:45:21,496] [INFO] Task succeeded: Blastn
[2023-03-17 07:45:21,497] [INFO] Selected 16 target genomes.
[2023-03-17 07:45:21,497] [INFO] Target genome list was writen to OceanDNA-b3314/target_genomes_gtdb.txt
[2023-03-17 07:45:21,522] [INFO] Task started: fastANI
[2023-03-17 07:45:21,522] [INFO] Running command: fastANI --query /var/lib/cwl/stg353d2aba-4f9d-477a-b4d8-97e71cc8fd9c/OceanDNA-b3314.fa --refList OceanDNA-b3314/target_genomes_gtdb.txt --output OceanDNA-b3314/fastani_result_gtdb.tsv --threads 1
[2023-03-17 07:45:31,842] [INFO] Task succeeded: fastANI
[2023-03-17 07:45:31,851] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 07:45:31,851] [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_018275325.1	s__Nocardioides sp018275325	84.6981	207	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004137255.1	s__Nocardioides oleivorans	84.654	207	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017310035.1	s__Nocardioides sp017310035	84.5229	199	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425025.1	s__Nocardioides sp001425025	84.4971	199	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653115.1	s__Nocardioides flavus	84.4771	194	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105585.1	s__Nocardioides exalbidus	84.4322	215	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907475.1	s__Nocardioides cavernae	84.3375	204	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004137245.1	s__Nocardioides glacieisoli	84.2385	194	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410035.1	s__Nocardioides cavernae_A	84.2363	206	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155375.1	s__Nocardioides sp013155375	84.234	202	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779665.1	s__Nocardioides hwasunensis	84.1456	210	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016735675.1	s__Nocardioides sp016735675	84.1193	196	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112035.1	s__Nocardioides alpinus	83.9655	198	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	99.99	99.99	1.00	1.00	2	-
GCF_017916455.1	s__Nocardioides sp017916455	83.9159	188	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.92	98.92	0.96	0.96	2	-
GCF_017872795.1	s__Nocardioides sp017872795	83.7472	197	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017916425.1	s__Nocardioides sp017916425	83.6824	192	240	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 07:45:31,852] [INFO] GTDB search result was written to OceanDNA-b3314/result_gtdb.tsv
[2023-03-17 07:45:31,852] [INFO] ===== GTDB Search completed =====
[2023-03-17 07:45:31,853] [INFO] DFAST_QC result json was written to OceanDNA-b3314/dqc_result.json
[2023-03-17 07:45:31,854] [INFO] DFAST_QC completed!
[2023-03-17 07:45:31,854] [INFO] Total running time: 0h0m55s