[2023-03-18 00:05:54,431] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:05:54,431] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:05:54,431] [INFO] DQC Reference Directory: /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference
[2023-03-18 00:05:55,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:05:55,536] [INFO] Task started: Prodigal
[2023-03-18 00:05:55,536] [INFO] Running command: cat /var/lib/cwl/stg21c11b77-4319-4e16-bf0b-4b6548e76ea1/OceanDNA-b25927.fa | prodigal -d OceanDNA-b25927/cds.fna -a OceanDNA-b25927/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:06:00,387] [INFO] Task succeeded: Prodigal
[2023-03-18 00:06:00,387] [INFO] Task started: HMMsearch
[2023-03-18 00:06:00,387] [INFO] Running command: hmmsearch --tblout OceanDNA-b25927/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/reference_markers.hmm OceanDNA-b25927/protein.faa > /dev/null
[2023-03-18 00:06:00,530] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:06:00,531] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg21c11b77-4319-4e16-bf0b-4b6548e76ea1/OceanDNA-b25927.fa]
[2023-03-18 00:06:00,541] [INFO] Query marker FASTA was written to OceanDNA-b25927/markers.fasta
[2023-03-18 00:06:00,542] [INFO] Task started: Blastn
[2023-03-18 00:06:00,542] [INFO] Running command: blastn -query OceanDNA-b25927/markers.fasta -db /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/reference_markers.fasta -out OceanDNA-b25927/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:00,990] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:00,991] [INFO] Selected 22 target genomes.
[2023-03-18 00:06:00,991] [INFO] Target genome list was writen to OceanDNA-b25927/target_genomes.txt
[2023-03-18 00:06:01,009] [INFO] Task started: fastANI
[2023-03-18 00:06:01,009] [INFO] Running command: fastANI --query /var/lib/cwl/stg21c11b77-4319-4e16-bf0b-4b6548e76ea1/OceanDNA-b25927.fa --refList OceanDNA-b25927/target_genomes.txt --output OceanDNA-b25927/fastani_result.tsv --threads 1
[2023-03-18 00:06:11,718] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:11,718] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:06:11,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:06:11,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:06:11,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 00:06:11,719] [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
--------------------------------------------------------------------------------
[2023-03-18 00:06:11,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-b25927/tc_result.tsv
[2023-03-18 00:06:11,719] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:06:11,719] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:06:11,719] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/checkm_data
[2023-03-18 00:06:11,722] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:06:11,778] [INFO] Task started: CheckM
[2023-03-18 00:06:11,779] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b25927/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b25927/checkm_input OceanDNA-b25927/checkm_result
[2023-03-18 00:06:30,211] [INFO] Task succeeded: CheckM
[2023-03-18 00:06:30,211] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 57.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 00:06:30,223] [INFO] ===== Completeness check finished =====
[2023-03-18 00:06:30,223] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:06:30,223] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b25927/markers.fasta)
[2023-03-18 00:06:30,224] [INFO] Task started: Blastn
[2023-03-18 00:06:30,225] [INFO] Running command: blastn -query OceanDNA-b25927/markers.fasta -db /var/lib/cwl/stg292d034c-25bb-46db-b57c-e28a0787e88a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b25927/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:06:30,657] [INFO] Task succeeded: Blastn
[2023-03-18 00:06:30,661] [INFO] Selected 24 target genomes.
[2023-03-18 00:06:30,662] [INFO] Target genome list was writen to OceanDNA-b25927/target_genomes_gtdb.txt
[2023-03-18 00:06:30,688] [INFO] Task started: fastANI
[2023-03-18 00:06:30,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg21c11b77-4319-4e16-bf0b-4b6548e76ea1/OceanDNA-b25927.fa --refList OceanDNA-b25927/target_genomes_gtdb.txt --output OceanDNA-b25927/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:06:36,951] [INFO] Task succeeded: fastANI
[2023-03-18 00:06:36,960] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:06:36,960] [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_905182395.1	s__CAJJBL01 sp905182395	78.7167	118	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__CAJJBL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000384615.1	s__AAA536-G10 sp000384615	77.083	83	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003282435.1	s__AAA536-G10 sp003282435	76.8927	63	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003278095.1	s__AAA536-G10 sp003278095	76.891	93	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	97.84	95.67	0.90	0.81	3	-
GCA_902583415.1	s__AAA536-G10 sp902583415	76.7719	57	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902543145.1	s__AAA536-G10 sp902543145	76.6908	59	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	99.74	99.74	0.81	0.81	2	-
GCA_000421325.1	s__AAA536-G10 sp000421325	76.6028	79	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003284565.1	s__AAA536-G10 sp003284565	76.5041	76	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902619805.1	s__AAA536-G10 sp902619805	76.4439	74	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902589185.1	s__AAA536-G10 sp902589185	76.4349	59	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902623995.1	s__AAA536-G10 sp902623995	76.3717	80	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	98.83	98.83	0.84	0.84	2	-
GCA_902622875.1	s__AAA536-G10 sp902622875	76.367	86	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902592615.1	s__AAA536-G10 sp902592615	76.299	66	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003283875.1	s__AAA536-G10 sp003283875	75.9174	59	299	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Puniceispirillales;f__AAA536-G10;g__AAA536-G10	95.0	95.33	95.28	0.67	0.61	3	-
--------------------------------------------------------------------------------
[2023-03-18 00:06:36,961] [INFO] GTDB search result was written to OceanDNA-b25927/result_gtdb.tsv
[2023-03-18 00:06:36,963] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:06:36,966] [INFO] DFAST_QC result json was written to OceanDNA-b25927/dqc_result.json
[2023-03-18 00:06:36,966] [INFO] DFAST_QC completed!
[2023-03-18 00:06:36,966] [INFO] Total running time: 0h0m43s