[2023-03-16 18:51:07,839] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:51:07,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:51:07,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference
[2023-03-16 18:51:08,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:51:08,958] [INFO] Task started: Prodigal
[2023-03-16 18:51:08,958] [INFO] Running command: cat /var/lib/cwl/stgba19980c-6e09-4d12-911c-33a205e05462/OceanDNA-b24040.fa | prodigal -d OceanDNA-b24040/cds.fna -a OceanDNA-b24040/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:51:17,433] [INFO] Task succeeded: Prodigal
[2023-03-16 18:51:17,433] [INFO] Task started: HMMsearch
[2023-03-16 18:51:17,433] [INFO] Running command: hmmsearch --tblout OceanDNA-b24040/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/reference_markers.hmm OceanDNA-b24040/protein.faa > /dev/null
[2023-03-16 18:51:17,559] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:51:17,560] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgba19980c-6e09-4d12-911c-33a205e05462/OceanDNA-b24040.fa]
[2023-03-16 18:51:17,574] [INFO] Query marker FASTA was written to OceanDNA-b24040/markers.fasta
[2023-03-16 18:51:17,575] [INFO] Task started: Blastn
[2023-03-16 18:51:17,575] [INFO] Running command: blastn -query OceanDNA-b24040/markers.fasta -db /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/reference_markers.fasta -out OceanDNA-b24040/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:51:18,095] [INFO] Task succeeded: Blastn
[2023-03-16 18:51:18,096] [INFO] Selected 10 target genomes.
[2023-03-16 18:51:18,096] [INFO] Target genome list was writen to OceanDNA-b24040/target_genomes.txt
[2023-03-16 18:51:18,101] [INFO] Task started: fastANI
[2023-03-16 18:51:18,101] [INFO] Running command: fastANI --query /var/lib/cwl/stgba19980c-6e09-4d12-911c-33a205e05462/OceanDNA-b24040.fa --refList OceanDNA-b24040/target_genomes.txt --output OceanDNA-b24040/fastani_result.tsv --threads 1
[2023-03-16 18:51:23,964] [INFO] Task succeeded: fastANI
[2023-03-16 18:51:23,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:51:23,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:51:23,972] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:51:23,972] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:51:23,972] [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
Parvularcula dongshanensis	strain=DSM 102850	GCA_014199615.1	1173995	1173995	type	True	79.187	255	506	95	below_threshold
Parvularcula oceani	strain=JLT2013	GCA_000733125.1	1247963	1247963	type	True	78.3215	253	506	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_014534785.1	1526572	1526572	type	True	76.1074	56	506	95	below_threshold
Aquisalinus flavus	strain=CGMCC 1.12921	GCA_014640095.1	1526572	1526572	type	True	76.1074	56	506	95	below_threshold
Aquisalinus flavus	strain=D11M-2	GCA_022559625.1	1526572	1526572	type	True	76.0912	55	506	95	below_threshold
Brevundimonas guildfordensis	strain=Sa3CVA3	GCA_014836405.1	2762241	2762241	type	True	75.7465	61	506	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.1914	124	506	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	75.1213	89	506	95	below_threshold
Microvirga splendida	strain=BT325	GCA_016427565.1	2795727	2795727	type	True	75.0441	52	506	95	below_threshold
Aurantimonas endophytica	strain=KCTC 52296	GCA_024105745.1	1522175	1522175	type	True	74.9971	60	506	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:51:23,972] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24040/tc_result.tsv
[2023-03-16 18:51:23,972] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:51:23,972] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:51:23,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/checkm_data
[2023-03-16 18:51:23,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:51:23,976] [INFO] Task started: CheckM
[2023-03-16 18:51:23,976] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24040/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24040/checkm_input OceanDNA-b24040/checkm_result
[2023-03-16 18:51:49,587] [INFO] Task succeeded: CheckM
[2023-03-16 18:51:49,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 39.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:51:49,589] [INFO] ===== Completeness check finished =====
[2023-03-16 18:51:49,589] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:51:49,589] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24040/markers.fasta)
[2023-03-16 18:51:49,590] [INFO] Task started: Blastn
[2023-03-16 18:51:49,590] [INFO] Running command: blastn -query OceanDNA-b24040/markers.fasta -db /var/lib/cwl/stg6fe3065a-924d-40c4-8c71-865aa43fb858/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24040/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:51:50,385] [INFO] Task succeeded: Blastn
[2023-03-16 18:51:50,386] [INFO] Selected 8 target genomes.
[2023-03-16 18:51:50,386] [INFO] Target genome list was writen to OceanDNA-b24040/target_genomes_gtdb.txt
[2023-03-16 18:51:50,392] [INFO] Task started: fastANI
[2023-03-16 18:51:50,392] [INFO] Running command: fastANI --query /var/lib/cwl/stgba19980c-6e09-4d12-911c-33a205e05462/OceanDNA-b24040.fa --refList OceanDNA-b24040/target_genomes_gtdb.txt --output OceanDNA-b24040/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:51:58,534] [INFO] Task succeeded: fastANI
[2023-03-16 18:51:58,540] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 18:51:58,540] [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
GCF_014199615.1	s__Parvularcula dongshanensis	79.2057	254	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733125.1	s__Parvularcula oceani	78.3065	254	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Parvularcula	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014640095.1	s__Aquisalinus flavus	76.1378	55	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Aquisalinus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001657385.1	s__Marinicaulis sp001657385	75.4671	82	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Parvularculaceae;g__Marinicaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	75.3419	108	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122085.1	s__WD6-1 sp003122085	75.3408	87	506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__WD6-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:51:58,540] [INFO] GTDB search result was written to OceanDNA-b24040/result_gtdb.tsv
[2023-03-16 18:51:58,540] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:51:58,542] [INFO] DFAST_QC result json was written to OceanDNA-b24040/dqc_result.json
[2023-03-16 18:51:58,542] [INFO] DFAST_QC completed!
[2023-03-16 18:51:58,542] [INFO] Total running time: 0h0m51s