[2023-03-16 09:43:37,171] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:43:37,171] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:43:37,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference
[2023-03-16 09:43:39,239] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:43:39,239] [INFO] Task started: Prodigal
[2023-03-16 09:43:39,239] [INFO] Running command: cat /var/lib/cwl/stgdd31b551-8e60-4cae-b1cc-5b2bc20504b1/OceanDNA-b22296.fa | prodigal -d OceanDNA-b22296/cds.fna -a OceanDNA-b22296/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:44:00,007] [INFO] Task succeeded: Prodigal
[2023-03-16 09:44:00,007] [INFO] Task started: HMMsearch
[2023-03-16 09:44:00,007] [INFO] Running command: hmmsearch --tblout OceanDNA-b22296/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/reference_markers.hmm OceanDNA-b22296/protein.faa > /dev/null
[2023-03-16 09:44:00,215] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:44:00,216] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgdd31b551-8e60-4cae-b1cc-5b2bc20504b1/OceanDNA-b22296.fa]
[2023-03-16 09:44:00,241] [INFO] Query marker FASTA was written to OceanDNA-b22296/markers.fasta
[2023-03-16 09:44:00,242] [INFO] Task started: Blastn
[2023-03-16 09:44:00,242] [INFO] Running command: blastn -query OceanDNA-b22296/markers.fasta -db /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/reference_markers.fasta -out OceanDNA-b22296/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:44:00,697] [INFO] Task succeeded: Blastn
[2023-03-16 09:44:00,697] [INFO] Selected 15 target genomes.
[2023-03-16 09:44:00,698] [INFO] Target genome list was writen to OceanDNA-b22296/target_genomes.txt
[2023-03-16 09:44:00,930] [INFO] Task started: fastANI
[2023-03-16 09:44:00,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd31b551-8e60-4cae-b1cc-5b2bc20504b1/OceanDNA-b22296.fa --refList OceanDNA-b22296/target_genomes.txt --output OceanDNA-b22296/fastani_result.tsv --threads 1
[2023-03-16 09:44:13,589] [INFO] Task succeeded: fastANI
[2023-03-16 09:44:13,590] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:44:13,590] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:44:13,597] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:44:13,597] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:44:13,597] [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
Algisphaera agarilytica	strain=DSM 103725	GCA_014207595.1	1385975	1385975	type	True	75.8196	68	1108	95	below_threshold
Humisphaera borealis	strain=M1803	GCA_015169395.1	2807512	2807512	type	True	75.8012	120	1108	95	below_threshold
Phycisphaera mikurensis	strain=NBRC 102666	GCA_000284115.1	547188	547188	type	True	75.205	85	1108	95	below_threshold
Phycisphaera mikurensis	strain=DSM 103959	GCA_014207395.1	547188	547188	type	True	75.2044	85	1108	95	below_threshold
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	74.8607	84	1108	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7338	90	1108	95	below_threshold
Aquibium microcysteis	strain=NIBR3	GCA_014495845.1	675281	675281	type	True	74.7072	50	1108	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.6952	84	1108	95	below_threshold
Microbispora camponoti	strain=2C-HV3	GCA_014712745.1	1677852	1677852	type	True	74.616	65	1108	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:44:13,597] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22296/tc_result.tsv
[2023-03-16 09:44:13,597] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:44:13,597] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:44:13,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/checkm_data
[2023-03-16 09:44:13,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:44:13,604] [INFO] Task started: CheckM
[2023-03-16 09:44:13,604] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22296/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22296/checkm_input OceanDNA-b22296/checkm_result
[2023-03-16 09:45:05,835] [INFO] Task succeeded: CheckM
[2023-03-16 09:45:05,836] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.87%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:45:05,945] [INFO] ===== Completeness check finished =====
[2023-03-16 09:45:05,946] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:45:05,946] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22296/markers.fasta)
[2023-03-16 09:45:05,947] [INFO] Task started: Blastn
[2023-03-16 09:45:05,947] [INFO] Running command: blastn -query OceanDNA-b22296/markers.fasta -db /var/lib/cwl/stg29943033-d576-4c7f-a0b9-9d15035e9a5d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22296/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:45:06,466] [INFO] Task succeeded: Blastn
[2023-03-16 09:45:06,475] [INFO] Selected 21 target genomes.
[2023-03-16 09:45:06,475] [INFO] Target genome list was writen to OceanDNA-b22296/target_genomes_gtdb.txt
[2023-03-16 09:45:06,520] [INFO] Task started: fastANI
[2023-03-16 09:45:06,520] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd31b551-8e60-4cae-b1cc-5b2bc20504b1/OceanDNA-b22296.fa --refList OceanDNA-b22296/target_genomes_gtdb.txt --output OceanDNA-b22296/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:45:19,593] [INFO] Task succeeded: fastANI
[2023-03-16 09:45:19,599] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:45:19,599] [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_014207595.1	s__Algisphaera agarilytica	75.8196	68	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Algisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015169395.1	s__Humisphaera borealis	75.8012	120	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Tepidisphaerales;f__Tepidisphaeraceae;g__Humisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891095.1	s__QWPT01 sp903891095	75.4753	65	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	99.40	98.92	0.94	0.91	5	-
GCA_007693965.1	s__RECQ01 sp007693965	75.2232	53	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__UBA1924;g__RECQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000284115.1	s__Phycisphaera mikurensis	75.1995	86	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__Phycisphaeraceae;g__Phycisphaera	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017859745.1	s__VGXO01 sp017859745	74.9702	53	1108	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__VGXO01	95.0	99.59	99.54	0.95	0.94	4	-
GCF_000522985.1	s__Gemmatirosa kalamazoonesis	74.7371	89	1108	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatirosa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016197405.1	s__Mycobacterium sp016197405	74.5706	52	1108	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 09:45:19,602] [INFO] GTDB search result was written to OceanDNA-b22296/result_gtdb.tsv
[2023-03-16 09:45:19,607] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:45:19,612] [INFO] DFAST_QC result json was written to OceanDNA-b22296/dqc_result.json
[2023-03-16 09:45:19,612] [INFO] DFAST_QC completed!
[2023-03-16 09:45:19,612] [INFO] Total running time: 0h1m42s