[2023-03-18 04:16:53,143] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:16:53,144] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:16:53,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference
[2023-03-18 04:16:54,279] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:16:54,279] [INFO] Task started: Prodigal
[2023-03-18 04:16:54,279] [INFO] Running command: cat /var/lib/cwl/stg216615f1-a82e-4142-8ca5-b678363f4dee/OceanDNA-b23905.fa | prodigal -d OceanDNA-b23905/cds.fna -a OceanDNA-b23905/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:17:07,179] [INFO] Task succeeded: Prodigal
[2023-03-18 04:17:07,179] [INFO] Task started: HMMsearch
[2023-03-18 04:17:07,179] [INFO] Running command: hmmsearch --tblout OceanDNA-b23905/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/reference_markers.hmm OceanDNA-b23905/protein.faa > /dev/null
[2023-03-18 04:17:07,359] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:17:07,360] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg216615f1-a82e-4142-8ca5-b678363f4dee/OceanDNA-b23905.fa]
[2023-03-18 04:17:07,374] [INFO] Query marker FASTA was written to OceanDNA-b23905/markers.fasta
[2023-03-18 04:17:07,375] [INFO] Task started: Blastn
[2023-03-18 04:17:07,375] [INFO] Running command: blastn -query OceanDNA-b23905/markers.fasta -db /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/reference_markers.fasta -out OceanDNA-b23905/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:07,961] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:07,962] [INFO] Selected 26 target genomes.
[2023-03-18 04:17:07,962] [INFO] Target genome list was writen to OceanDNA-b23905/target_genomes.txt
[2023-03-18 04:17:07,980] [INFO] Task started: fastANI
[2023-03-18 04:17:07,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg216615f1-a82e-4142-8ca5-b678363f4dee/OceanDNA-b23905.fa --refList OceanDNA-b23905/target_genomes.txt --output OceanDNA-b23905/fastani_result.tsv --threads 1
[2023-03-18 04:17:22,077] [INFO] Task succeeded: fastANI
[2023-03-18 04:17:22,077] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:17:22,078] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:17:22,083] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:17:22,084] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:17:22,084] [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
Hyphobacterium indicum	strain=2ED5	GCA_003129605.1	2162714	2162714	type	True	77.0833	166	682	95	below_threshold
Maricaulis maris	strain=DSM 4734	GCA_003634045.1	74318	74318	type	True	76.5156	115	682	95	below_threshold
Maricaulis salignorans	strain=DSM 16077	GCA_900103475.1	144026	144026	type	True	76.4495	110	682	95	below_threshold
Maricaulis alexandrii	strain=LZ-16-1	GCA_005871165.1	2570354	2570354	type	True	76.4044	97	682	95	below_threshold
Glycocaulis albus	strain=CGMCC 1.12766	GCA_014639075.1	1382801	1382801	type	True	76.2643	72	682	95	below_threshold
Marinicauda pacifica	strain=CGMCC 1.11031	GCA_014636415.1	1133559	1133559	type	True	76.0947	71	682	95	below_threshold
Marinicauda pacifica	strain=P-1 km-3	GCA_004793635.1	1133559	1133559	type	True	76.0947	71	682	95	below_threshold
Euryhalocaulis caribicus	strain=JL2009	GCA_000412185.1	1161401	1161401	type	True	75.6455	54	682	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:17:22,084] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23905/tc_result.tsv
[2023-03-18 04:17:22,084] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:17:22,084] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:17:22,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/checkm_data
[2023-03-18 04:17:22,085] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:17:22,147] [INFO] Task started: CheckM
[2023-03-18 04:17:22,147] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23905/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23905/checkm_input OceanDNA-b23905/checkm_result
[2023-03-18 04:17:58,261] [INFO] Task succeeded: CheckM
[2023-03-18 04:17:58,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:17:58,264] [INFO] ===== Completeness check finished =====
[2023-03-18 04:17:58,264] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:17:58,264] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23905/markers.fasta)
[2023-03-18 04:17:58,265] [INFO] Task started: Blastn
[2023-03-18 04:17:58,265] [INFO] Running command: blastn -query OceanDNA-b23905/markers.fasta -db /var/lib/cwl/stg9396bde2-ee6a-4321-be65-5ab4de48ce79/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23905/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:17:59,219] [INFO] Task succeeded: Blastn
[2023-03-18 04:17:59,219] [INFO] Selected 21 target genomes.
[2023-03-18 04:17:59,220] [INFO] Target genome list was writen to OceanDNA-b23905/target_genomes_gtdb.txt
[2023-03-18 04:17:59,428] [INFO] Task started: fastANI
[2023-03-18 04:17:59,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg216615f1-a82e-4142-8ca5-b678363f4dee/OceanDNA-b23905.fa --refList OceanDNA-b23905/target_genomes_gtdb.txt --output OceanDNA-b23905/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:18:11,904] [INFO] Task succeeded: fastANI
[2023-03-18 04:18:11,913] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:18:11,913] [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_002783385.1	s__Hyphobacterium sp002783385	77.1369	98	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124665.1	s__Hyphobacterium sp016124665	77.1291	148	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129605.1	s__Hyphobacterium indicum	77.0833	166	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323565.1	s__Hyphobacterium sp014323565	76.7681	155	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015665295.1	s__Maricaulis sp015665295	76.6612	94	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692855.1	s__Hyphobacterium sp002692855	76.603	140	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	99.83	99.83	0.96	0.96	2	-
GCA_016124205.1	s__Hyphobacterium sp016124205	76.6012	116	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Hyphobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634045.1	s__Maricaulis maris	76.5156	115	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.04	98.04	0.96	0.96	2	-
GCF_016817355.1	s__Maricaulis parjimensis	76.509	100	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103475.1	s__Maricaulis salignorans	76.4495	110	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000014745.1	s__Maricaulis maris_A	76.4463	98	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	98.51	98.49	0.94	0.92	3	-
GCF_005871165.1	s__Maricaulis sp005871165	76.4044	97	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905480005.1	s__Maricaulis sp905480005	76.3201	93	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017643475.1	s__Maricaulis sp017643475	76.0705	80	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642925.1	s__Maricaulis sp017642925	76.0145	102	682	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Maricaulaceae;g__Maricaulis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:18:11,913] [INFO] GTDB search result was written to OceanDNA-b23905/result_gtdb.tsv
[2023-03-18 04:18:11,913] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:18:11,915] [INFO] DFAST_QC result json was written to OceanDNA-b23905/dqc_result.json
[2023-03-18 04:18:11,915] [INFO] DFAST_QC completed!
[2023-03-18 04:18:11,915] [INFO] Total running time: 0h1m19s