[2023-03-17 02:31:12,847] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:31:12,847] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:31:12,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference
[2023-03-17 02:31:14,377] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:31:14,377] [INFO] Task started: Prodigal
[2023-03-17 02:31:14,377] [INFO] Running command: cat /var/lib/cwl/stgf127576c-2514-4404-b59f-ccff55d24b4a/OceanDNA-b35991.fa | prodigal -d OceanDNA-b35991/cds.fna -a OceanDNA-b35991/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:31:22,628] [INFO] Task succeeded: Prodigal
[2023-03-17 02:31:22,628] [INFO] Task started: HMMsearch
[2023-03-17 02:31:22,628] [INFO] Running command: hmmsearch --tblout OceanDNA-b35991/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/reference_markers.hmm OceanDNA-b35991/protein.faa > /dev/null
[2023-03-17 02:31:22,813] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:31:22,813] [INFO] Found 6/6 markers.
[2023-03-17 02:31:22,828] [INFO] Query marker FASTA was written to OceanDNA-b35991/markers.fasta
[2023-03-17 02:31:22,828] [INFO] Task started: Blastn
[2023-03-17 02:31:22,828] [INFO] Running command: blastn -query OceanDNA-b35991/markers.fasta -db /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/reference_markers.fasta -out OceanDNA-b35991/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:31:23,359] [INFO] Task succeeded: Blastn
[2023-03-17 02:31:23,360] [INFO] Selected 33 target genomes.
[2023-03-17 02:31:23,360] [INFO] Target genome list was writen to OceanDNA-b35991/target_genomes.txt
[2023-03-17 02:31:23,379] [INFO] Task started: fastANI
[2023-03-17 02:31:23,379] [INFO] Running command: fastANI --query /var/lib/cwl/stgf127576c-2514-4404-b59f-ccff55d24b4a/OceanDNA-b35991.fa --refList OceanDNA-b35991/target_genomes.txt --output OceanDNA-b35991/fastani_result.tsv --threads 1
[2023-03-17 02:31:41,831] [INFO] Task succeeded: fastANI
[2023-03-17 02:31:41,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:31:41,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:31:41,834] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:31:41,835] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 02:31:41,835] [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
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	77.8126	72	482	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.381	52	482	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:31:41,835] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35991/tc_result.tsv
[2023-03-17 02:31:41,835] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:31:41,835] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:31:41,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/checkm_data
[2023-03-17 02:31:41,836] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:31:41,842] [INFO] Task started: CheckM
[2023-03-17 02:31:41,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35991/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35991/checkm_input OceanDNA-b35991/checkm_result
[2023-03-17 02:32:07,531] [INFO] Task succeeded: CheckM
[2023-03-17 02:32:07,532] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 3.01%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-03-17 02:32:07,534] [INFO] ===== Completeness check finished =====
[2023-03-17 02:32:07,534] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:32:07,534] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35991/markers.fasta)
[2023-03-17 02:32:07,536] [INFO] Task started: Blastn
[2023-03-17 02:32:07,536] [INFO] Running command: blastn -query OceanDNA-b35991/markers.fasta -db /var/lib/cwl/stg4f64d52b-8462-49da-8595-d8f0c512d7a1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35991/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:32:08,351] [INFO] Task succeeded: Blastn
[2023-03-17 02:32:08,352] [INFO] Selected 14 target genomes.
[2023-03-17 02:32:08,352] [INFO] Target genome list was writen to OceanDNA-b35991/target_genomes_gtdb.txt
[2023-03-17 02:32:08,601] [INFO] Task started: fastANI
[2023-03-17 02:32:08,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgf127576c-2514-4404-b59f-ccff55d24b4a/OceanDNA-b35991.fa --refList OceanDNA-b35991/target_genomes_gtdb.txt --output OceanDNA-b35991/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:32:16,260] [INFO] Task succeeded: fastANI
[2023-03-17 02:32:16,269] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:32:16,270] [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_903939355.1	s__KS41 sp903939355	96.1327	358	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.41	98.41	0.76	0.76	2	conclusive
GCA_903908165.1	s__KS41 sp903908165	84.9298	393	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.39	98.42	0.88	0.71	10	-
GCA_903903365.1	s__KS41 sp903903365	78.6516	170	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903873045.1	s__KS41 sp903873045	78.4682	173	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863905.1	s__KS41 sp903863905	78.0731	114	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.63	99.29	0.91	0.83	33	-
GCA_903839795.1	s__KS41 sp903839795	78.0603	159	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903859415.1	s__KS41 sp903859415	77.9792	144	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.28	98.83	0.89	0.85	3	-
GCA_903866825.1	s__KS41 sp903866825	77.697	141	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.82	99.82	0.85	0.85	2	-
GCA_003584875.1	s__KS41 sp003584875	77.6625	103	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	98.94	98.69	0.84	0.76	9	-
GCA_903839855.1	s__KS41 sp903839855	77.6362	133	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.93	99.90	0.95	0.94	3	-
GCA_003584865.1	s__KS41 sp003584865	77.52	97	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	97.03	0.84	0.75	9	-
GCA_903934035.1	s__KS41 sp903934035	77.449	105	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.03	98.98	0.89	0.84	3	-
GCA_903873165.1	s__KS41 sp903873165	77.1737	113	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	99.76	99.76	0.93	0.93	2	-
GCA_903903765.1	s__KS41 sp903903765	76.9979	66	482	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__KS41	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:32:16,270] [INFO] GTDB search result was written to OceanDNA-b35991/result_gtdb.tsv
[2023-03-17 02:32:16,270] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:32:16,271] [INFO] DFAST_QC result json was written to OceanDNA-b35991/dqc_result.json
[2023-03-17 02:32:16,271] [INFO] DFAST_QC completed!
[2023-03-17 02:32:16,271] [INFO] Total running time: 0h1m3s