[2023-03-15 16:15:00,907] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:15:00,907] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:15:00,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference
[2023-03-15 16:15:01,985] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:15:01,985] [INFO] Task started: Prodigal
[2023-03-15 16:15:01,985] [INFO] Running command: cat /var/lib/cwl/stga439a8ab-2897-4b12-b250-9f86e6552f77/OceanDNA-b32762.fa | prodigal -d OceanDNA-b32762/cds.fna -a OceanDNA-b32762/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:15:08,895] [INFO] Task succeeded: Prodigal
[2023-03-15 16:15:08,895] [INFO] Task started: HMMsearch
[2023-03-15 16:15:08,895] [INFO] Running command: hmmsearch --tblout OceanDNA-b32762/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/reference_markers.hmm OceanDNA-b32762/protein.faa > /dev/null
[2023-03-15 16:15:09,040] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:15:09,041] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga439a8ab-2897-4b12-b250-9f86e6552f77/OceanDNA-b32762.fa]
[2023-03-15 16:15:09,055] [INFO] Query marker FASTA was written to OceanDNA-b32762/markers.fasta
[2023-03-15 16:15:09,056] [INFO] Task started: Blastn
[2023-03-15 16:15:09,056] [INFO] Running command: blastn -query OceanDNA-b32762/markers.fasta -db /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/reference_markers.fasta -out OceanDNA-b32762/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:09,665] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:09,666] [INFO] Selected 25 target genomes.
[2023-03-15 16:15:09,666] [INFO] Target genome list was writen to OceanDNA-b32762/target_genomes.txt
[2023-03-15 16:15:09,681] [INFO] Task started: fastANI
[2023-03-15 16:15:09,681] [INFO] Running command: fastANI --query /var/lib/cwl/stga439a8ab-2897-4b12-b250-9f86e6552f77/OceanDNA-b32762.fa --refList OceanDNA-b32762/target_genomes.txt --output OceanDNA-b32762/fastani_result.tsv --threads 1
[2023-03-15 16:15:31,130] [INFO] Task succeeded: fastANI
[2023-03-15 16:15:31,130] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:15:31,131] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:15:31,136] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:15:31,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:15:31,136] [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
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	76.1242	58	307	95	below_threshold
Hypericibacter adhaerens	strain=R5959	GCA_008728835.1	2602016	2602016	type	True	75.9286	52	307	95	below_threshold
Azospirillum thermophilum	strain=CFH 70021	GCA_003130795.1	2202148	2202148	type	True	75.9216	55	307	95	below_threshold
Inquilinus limosus	strain=DSM 16000	GCA_000423185.1	171674	171674	type	True	75.8632	60	307	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.7919	50	307	95	below_threshold
Reyranella soli	strain=NBRC 108950	GCA_007992495.1	1230389	1230389	type	True	75.4472	54	307	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:15:31,137] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32762/tc_result.tsv
[2023-03-15 16:15:31,137] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:15:31,137] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:15:31,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/checkm_data
[2023-03-15 16:15:31,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:15:31,141] [INFO] Task started: CheckM
[2023-03-15 16:15:31,141] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32762/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32762/checkm_input OceanDNA-b32762/checkm_result
[2023-03-15 16:15:53,559] [INFO] Task succeeded: CheckM
[2023-03-15 16:15:53,560] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:15:53,562] [INFO] ===== Completeness check finished =====
[2023-03-15 16:15:53,562] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:15:53,562] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32762/markers.fasta)
[2023-03-15 16:15:53,564] [INFO] Task started: Blastn
[2023-03-15 16:15:53,564] [INFO] Running command: blastn -query OceanDNA-b32762/markers.fasta -db /var/lib/cwl/stg88a56f84-4d69-4a9f-a07b-7468c1bc77fc/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32762/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:15:54,577] [INFO] Task succeeded: Blastn
[2023-03-15 16:15:54,602] [INFO] Selected 10 target genomes.
[2023-03-15 16:15:54,602] [INFO] Target genome list was writen to OceanDNA-b32762/target_genomes_gtdb.txt
[2023-03-15 16:15:54,693] [INFO] Task started: fastANI
[2023-03-15 16:15:54,693] [INFO] Running command: fastANI --query /var/lib/cwl/stga439a8ab-2897-4b12-b250-9f86e6552f77/OceanDNA-b32762.fa --refList OceanDNA-b32762/target_genomes_gtdb.txt --output OceanDNA-b32762/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:16:00,691] [INFO] Task succeeded: fastANI
[2023-03-15 16:16:00,695] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 16:16:00,696] [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_018702955.1	s__UBA8079 sp018702955	79.4996	215	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.54	99.39	0.93	0.91	5	-
GCA_018667335.1	s__UBA8079 sp018667335	79.4269	215	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	99.89	99.79	0.96	0.96	6	-
GCA_002724635.1	s__UBA8079 sp002724635	79.3164	206	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727315.1	s__UBA8079 sp002727315	78.5036	153	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643325.1	s__JABJAG01 sp017643325	78.49	136	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__JABJAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722515.1	s__UBA8079 sp002722515	77.0626	92	307	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__UBA6615;f__UBA6615;g__UBA8079	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:16:00,696] [INFO] GTDB search result was written to OceanDNA-b32762/result_gtdb.tsv
[2023-03-15 16:16:00,696] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:16:00,697] [INFO] DFAST_QC result json was written to OceanDNA-b32762/dqc_result.json
[2023-03-15 16:16:00,697] [INFO] DFAST_QC completed!
[2023-03-15 16:16:00,697] [INFO] Total running time: 0h0m60s