[2023-03-15 11:36:00,601] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:36:00,603] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:36:00,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference
[2023-03-15 11:36:02,582] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:36:02,582] [INFO] Task started: Prodigal
[2023-03-15 11:36:02,583] [INFO] Running command: cat /var/lib/cwl/stg96bfec6e-ab4b-4ec3-bf90-4d954671fd19/OceanDNA-b46933.fa | prodigal -d OceanDNA-b46933/cds.fna -a OceanDNA-b46933/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:36:42,744] [INFO] Task succeeded: Prodigal
[2023-03-15 11:36:42,745] [INFO] Task started: HMMsearch
[2023-03-15 11:36:42,745] [INFO] Running command: hmmsearch --tblout OceanDNA-b46933/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/reference_markers.hmm OceanDNA-b46933/protein.faa > /dev/null
[2023-03-15 11:36:42,967] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:36:42,967] [INFO] Found 6/6 markers.
[2023-03-15 11:36:43,037] [INFO] Query marker FASTA was written to OceanDNA-b46933/markers.fasta
[2023-03-15 11:36:43,038] [INFO] Task started: Blastn
[2023-03-15 11:36:43,038] [INFO] Running command: blastn -query OceanDNA-b46933/markers.fasta -db /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/reference_markers.fasta -out OceanDNA-b46933/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:36:43,584] [INFO] Task succeeded: Blastn
[2023-03-15 11:36:43,602] [INFO] Selected 17 target genomes.
[2023-03-15 11:36:43,603] [INFO] Target genome list was writen to OceanDNA-b46933/target_genomes.txt
[2023-03-15 11:36:43,613] [INFO] Task started: fastANI
[2023-03-15 11:36:43,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bfec6e-ab4b-4ec3-bf90-4d954671fd19/OceanDNA-b46933.fa --refList OceanDNA-b46933/target_genomes.txt --output OceanDNA-b46933/fastani_result.tsv --threads 1
[2023-03-15 11:36:57,945] [INFO] Task succeeded: fastANI
[2023-03-15 11:36:57,945] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:36:57,945] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:36:57,949] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:36:57,949] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:36:57,949] [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
Luteolibacter luteus	strain=G-1-1-1	GCA_012913485.1	2728835	2728835	type	True	75.7008	53	1621	95	below_threshold
Haloferula rosea	strain=KCTC 22201	GCA_016595525.1	490093	490093	type	True	75.5568	54	1621	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:36:57,953] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46933/tc_result.tsv
[2023-03-15 11:36:57,958] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:36:57,958] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:36:57,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/checkm_data
[2023-03-15 11:36:57,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:36:57,980] [INFO] Task started: CheckM
[2023-03-15 11:36:57,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46933/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46933/checkm_input OceanDNA-b46933/checkm_result
[2023-03-15 11:38:33,500] [INFO] Task succeeded: CheckM
[2023-03-15 11:38:33,501] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:38:33,769] [INFO] ===== Completeness check finished =====
[2023-03-15 11:38:33,769] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:38:33,769] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46933/markers.fasta)
[2023-03-15 11:38:33,770] [INFO] Task started: Blastn
[2023-03-15 11:38:33,770] [INFO] Running command: blastn -query OceanDNA-b46933/markers.fasta -db /var/lib/cwl/stg27e1d17a-334e-429e-aa0f-a9047e9bc4a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46933/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:38:34,590] [INFO] Task succeeded: Blastn
[2023-03-15 11:38:34,602] [INFO] Selected 14 target genomes.
[2023-03-15 11:38:34,603] [INFO] Target genome list was writen to OceanDNA-b46933/target_genomes_gtdb.txt
[2023-03-15 11:38:34,644] [INFO] Task started: fastANI
[2023-03-15 11:38:34,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg96bfec6e-ab4b-4ec3-bf90-4d954671fd19/OceanDNA-b46933.fa --refList OceanDNA-b46933/target_genomes_gtdb.txt --output OceanDNA-b46933/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:38:45,648] [INFO] Task succeeded: fastANI
[2023-03-15 11:38:45,655] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 11:38:45,655] [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_013213905.1	s__Arctic95D-9 sp013213905	76.8486	260	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396885.1	s__Arctic95D-9 sp002396885	76.8095	248	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344525.1	s__Arctic95D-9 sp002344525	76.784	252	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795385.1	s__Arctic95D-9 sp016795385	76.7837	305	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012719225.1	s__Arctic95D-9 sp012719225	76.5609	220	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123695.1	s__Arctic95D-9 sp007123695	76.5269	179	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002288445.1	s__Arctic95D-9 sp002288445	76.4891	93	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002862135.1	s__Arctic95D-9 sp002862135	76.4564	148	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002698785.1	s__Arctic95D-9 sp002698785	76.3451	149	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__DEV007;g__Arctic95D-9	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012913485.1	s__Haloferula lutea	75.7008	53	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000739615.1	s__Haloferula sp000739615	75.458	56	1621	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Verrucomicrobiales;f__Akkermansiaceae;g__Haloferula	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:38:45,660] [INFO] GTDB search result was written to OceanDNA-b46933/result_gtdb.tsv
[2023-03-15 11:38:45,670] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:38:45,678] [INFO] DFAST_QC result json was written to OceanDNA-b46933/dqc_result.json
[2023-03-15 11:38:45,678] [INFO] DFAST_QC completed!
[2023-03-15 11:38:45,678] [INFO] Total running time: 0h2m45s