[2023-03-14 12:19:39,512] [INFO] DFAST_QC pipeline started.
[2023-03-14 12:19:39,513] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 12:19:39,513] [INFO] DQC Reference Directory: /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference
[2023-03-14 12:19:40,616] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 12:19:40,616] [INFO] Task started: Prodigal
[2023-03-14 12:19:40,616] [INFO] Running command: cat /var/lib/cwl/stg87d624ed-9f6c-43a0-a0ff-ba9e6a1c4af3/OceanDNA-b7917.fa | prodigal -d OceanDNA-b7917/cds.fna -a OceanDNA-b7917/protein.faa -g 11 -q > /dev/null
[2023-03-14 12:19:46,137] [INFO] Task succeeded: Prodigal
[2023-03-14 12:19:46,137] [INFO] Task started: HMMsearch
[2023-03-14 12:19:46,137] [INFO] Running command: hmmsearch --tblout OceanDNA-b7917/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/reference_markers.hmm OceanDNA-b7917/protein.faa > /dev/null
[2023-03-14 12:19:46,310] [INFO] Task succeeded: HMMsearch
[2023-03-14 12:19:46,310] [INFO] Found 6/6 markers.
[2023-03-14 12:19:46,322] [INFO] Query marker FASTA was written to OceanDNA-b7917/markers.fasta
[2023-03-14 12:19:46,323] [INFO] Task started: Blastn
[2023-03-14 12:19:46,323] [INFO] Running command: blastn -query OceanDNA-b7917/markers.fasta -db /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/reference_markers.fasta -out OceanDNA-b7917/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:19:46,915] [INFO] Task succeeded: Blastn
[2023-03-14 12:19:46,917] [INFO] Selected 28 target genomes.
[2023-03-14 12:19:46,918] [INFO] Target genome list was writen to OceanDNA-b7917/target_genomes.txt
[2023-03-14 12:19:46,935] [INFO] Task started: fastANI
[2023-03-14 12:19:46,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d624ed-9f6c-43a0-a0ff-ba9e6a1c4af3/OceanDNA-b7917.fa --refList OceanDNA-b7917/target_genomes.txt --output OceanDNA-b7917/fastani_result.tsv --threads 1
[2023-03-14 12:20:01,740] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:01,740] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 12:20:01,741] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 12:20:01,741] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 12:20:01,741] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 12:20:01,741] [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
--------------------------------------------------------------------------------
[2023-03-14 12:20:01,743] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7917/tc_result.tsv
[2023-03-14 12:20:01,744] [INFO] ===== Taxonomy check completed =====
[2023-03-14 12:20:01,744] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 12:20:01,744] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/checkm_data
[2023-03-14 12:20:01,747] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 12:20:01,751] [INFO] Task started: CheckM
[2023-03-14 12:20:01,751] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7917/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7917/checkm_input OceanDNA-b7917/checkm_result
[2023-03-14 12:20:21,729] [INFO] Task succeeded: CheckM
[2023-03-14 12:20:21,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 12:20:21,813] [INFO] ===== Completeness check finished =====
[2023-03-14 12:20:21,813] [INFO] ===== Start GTDB Search =====
[2023-03-14 12:20:21,813] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7917/markers.fasta)
[2023-03-14 12:20:21,815] [INFO] Task started: Blastn
[2023-03-14 12:20:21,815] [INFO] Running command: blastn -query OceanDNA-b7917/markers.fasta -db /var/lib/cwl/stg250ca7b9-bc9f-465e-b8e8-24ac3667f87f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7917/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 12:20:22,821] [INFO] Task succeeded: Blastn
[2023-03-14 12:20:22,825] [INFO] Selected 13 target genomes.
[2023-03-14 12:20:22,825] [INFO] Target genome list was writen to OceanDNA-b7917/target_genomes_gtdb.txt
[2023-03-14 12:20:22,841] [INFO] Task started: fastANI
[2023-03-14 12:20:22,841] [INFO] Running command: fastANI --query /var/lib/cwl/stg87d624ed-9f6c-43a0-a0ff-ba9e6a1c4af3/OceanDNA-b7917.fa --refList OceanDNA-b7917/target_genomes_gtdb.txt --output OceanDNA-b7917/fastani_result_gtdb.tsv --threads 1
[2023-03-14 12:20:26,245] [INFO] Task succeeded: fastANI
[2023-03-14 12:20:26,252] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 12:20:26,253] [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_902559035.1	s__MAG-121220-bin8 sp902559035	96.392	236	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.40	96.04	0.82	0.79	6	conclusive
GCA_902635895.1	s__MAG-121220-bin8 sp902635895	80.8083	160	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.57	96.57	0.70	0.70	2	-
GCA_016780345.1	s__MAG-121220-bin8 sp016780345	79.7131	168	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.67	99.67	0.79	0.79	2	-
GCA_902510655.1	s__MAG-121220-bin8 sp902510655	79.6438	120	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004214185.1	s__MAG-121220-bin8 sp004214185	79.581	168	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	96.26	95.81	0.84	0.82	5	-
GCA_905479415.1	s__MAG-121220-bin8 sp905479415	79.4662	166	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	98.94	98.70	0.82	0.77	8	-
GCA_002700465.1	s__MAG-121220-bin8 sp002700465	79.2809	133	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.15	98.67	0.80	0.80	3	-
GCA_905182765.1	s__MAG-121220-bin8 sp905182765	78.9408	171	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018662905.1	s__MAG-121220-bin8 sp018662905	78.3683	121	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.06	99.06	0.75	0.75	2	-
GCA_012959395.1	s__MAG-121220-bin8 sp012959395	77.4598	107	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	97.96	97.81	0.81	0.77	13	-
GCA_902511755.1	s__MAG-121220-bin8 sp902511755	77.444	84	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	99.22	98.71	0.74	0.72	3	-
GCA_002702895.1	s__MAG-121220-bin8 sp002702895	77.2836	123	276	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAG-121220-bin8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 12:20:26,254] [INFO] GTDB search result was written to OceanDNA-b7917/result_gtdb.tsv
[2023-03-14 12:20:26,254] [INFO] ===== GTDB Search completed =====
[2023-03-14 12:20:26,258] [INFO] DFAST_QC result json was written to OceanDNA-b7917/dqc_result.json
[2023-03-14 12:20:26,258] [INFO] DFAST_QC completed!
[2023-03-14 12:20:26,258] [INFO] Total running time: 0h0m47s