[2023-03-14 12:03:55,357] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:03:55,363] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:03:55,363] [INFO] DQC Reference Directory: /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference
[2023-03-14 12:03:56,865] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:03:56,865] [INFO] Task started: Prodigal
[2023-03-14 12:03:56,865] [INFO] Running command: cat /var/lib/cwl/stgca6816c0-74ec-4c64-b5b4-9e2fb487c3b1/OceanDNA-b23017.fa | prodigal -d OceanDNA-b23017/cds.fna -a OceanDNA-b23017/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:04:36,681] [INFO] Task succeeded: Prodigal
[2023-03-14 12:04:36,681] [INFO] Task started: HMMsearch
[2023-03-14 12:04:36,681] [INFO] Running command: hmmsearch --tblout OceanDNA-b23017/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/reference_markers.hmm OceanDNA-b23017/protein.faa > /dev/null
[2023-03-14 12:04:36,944] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:04:36,945] [INFO] Found 6/6 markers.
[2023-03-14 12:04:37,028] [INFO] Query marker FASTA was written to OceanDNA-b23017/markers.fasta
[2023-03-14 12:04:37,029] [INFO] Task started: Blastn
[2023-03-14 12:04:37,029] [INFO] Running command: blastn -query OceanDNA-b23017/markers.fasta -db /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/reference_markers.fasta -out OceanDNA-b23017/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:04:37,586] [INFO] Task succeeded: Blastn
[2023-03-14 12:04:37,600] [INFO] Selected 21 target genomes.
[2023-03-14 12:04:37,600] [INFO] Target genome list was writen to OceanDNA-b23017/target_genomes.txt
[2023-03-14 12:04:37,613] [INFO] Task started: fastANI
[2023-03-14 12:04:37,613] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6816c0-74ec-4c64-b5b4-9e2fb487c3b1/OceanDNA-b23017.fa --refList OceanDNA-b23017/target_genomes.txt --output OceanDNA-b23017/fastani_result.tsv --threads 1
[2023-03-14 12:04:55,227] [INFO] Task succeeded: fastANI
[2023-03-14 12:04:55,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:04:55,227] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:04:55,231] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:04:55,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 12:04:55,231] [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
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	74.7992	51	2033	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 12:04:55,235] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23017/tc_result.tsv
[2023-03-14 12:04:55,247] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:04:55,248] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:04:55,248] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/checkm_data
[2023-03-14 12:04:55,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:04:55,296] [INFO] Task started: CheckM
[2023-03-14 12:04:55,296] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23017/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23017/checkm_input OceanDNA-b23017/checkm_result
[2023-03-14 12:06:51,744] [INFO] Task succeeded: CheckM
[2023-03-14 12:06:51,744] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:06:51,774] [INFO] ===== Completeness check finished =====
[2023-03-14 12:06:51,774] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:06:51,774] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23017/markers.fasta)
[2023-03-14 12:06:51,775] [INFO] Task started: Blastn
[2023-03-14 12:06:51,775] [INFO] Running command: blastn -query OceanDNA-b23017/markers.fasta -db /var/lib/cwl/stga3cee5ef-d1c0-4db5-b439-960527a8e748/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23017/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:06:52,556] [INFO] Task succeeded: Blastn
[2023-03-14 12:06:52,562] [INFO] Selected 14 target genomes.
[2023-03-14 12:06:52,562] [INFO] Target genome list was writen to OceanDNA-b23017/target_genomes_gtdb.txt
[2023-03-14 12:06:52,572] [INFO] Task started: fastANI
[2023-03-14 12:06:52,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgca6816c0-74ec-4c64-b5b4-9e2fb487c3b1/OceanDNA-b23017.fa --refList OceanDNA-b23017/target_genomes_gtdb.txt --output OceanDNA-b23017/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:07:03,403] [INFO] Task succeeded: fastANI
[2023-03-14 12:07:03,410] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 12:07:03,411] [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_014237855.1	s__JABACD01 sp014237855	76.9457	213	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABACD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012959785.1	s__DUCM01 sp012959785	76.9269	196	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__DUCM01	95.0	99.99	99.99	0.99	0.99	2	-
GCA_002686265.1	s__GCA-2686265 sp002686265	76.4918	155	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	76.2458	133	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004357655.1	s__N075bin59 sp004357655	76.2244	75	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__N075bin59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795245.1	s__JAEUIA01 sp016795245	75.9963	82	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUIA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007751255.1	s__Pla86 sp007751255	75.9081	156	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla86	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.833	95	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009691855.1	s__JABFRZ01 sp009691855	75.8225	100	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714045.1	s__JADJNY01 sp016714045	75.6522	125	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016220035.1	s__JADJNY01 sp016220035	75.5213	86	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJNY01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013140785.1	s__JABFRZ01 sp013140785	75.5126	75	2033	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JABFRZ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:07:03,414] [INFO] GTDB search result was written to OceanDNA-b23017/result_gtdb.tsv
[2023-03-14 12:07:03,416] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:07:03,420] [INFO] DFAST_QC result json was written to OceanDNA-b23017/dqc_result.json
[2023-03-14 12:07:03,420] [INFO] DFAST_QC completed!
[2023-03-14 12:07:03,420] [INFO] Total running time: 0h3m8s