[2023-03-17 05:31:30,560] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:31:30,561] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:31:30,561] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference
[2023-03-17 05:31:33,265] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:31:33,266] [INFO] Task started: Prodigal
[2023-03-17 05:31:33,266] [INFO] Running command: cat /var/lib/cwl/stg4c995f46-8074-47d7-8677-ada7796e1234/OceanDNA-b22995.fa | prodigal -d OceanDNA-b22995/cds.fna -a OceanDNA-b22995/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:31:47,743] [INFO] Task succeeded: Prodigal
[2023-03-17 05:31:47,743] [INFO] Task started: HMMsearch
[2023-03-17 05:31:47,743] [INFO] Running command: hmmsearch --tblout OceanDNA-b22995/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/reference_markers.hmm OceanDNA-b22995/protein.faa > /dev/null
[2023-03-17 05:31:47,911] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:31:47,911] [INFO] Found 6/6 markers.
[2023-03-17 05:31:47,926] [INFO] Query marker FASTA was written to OceanDNA-b22995/markers.fasta
[2023-03-17 05:31:47,928] [INFO] Task started: Blastn
[2023-03-17 05:31:47,928] [INFO] Running command: blastn -query OceanDNA-b22995/markers.fasta -db /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/reference_markers.fasta -out OceanDNA-b22995/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:31:48,473] [INFO] Task succeeded: Blastn
[2023-03-17 05:31:48,474] [INFO] Selected 25 target genomes.
[2023-03-17 05:31:48,474] [INFO] Target genome list was writen to OceanDNA-b22995/target_genomes.txt
[2023-03-17 05:31:48,489] [INFO] Task started: fastANI
[2023-03-17 05:31:48,489] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c995f46-8074-47d7-8677-ada7796e1234/OceanDNA-b22995.fa --refList OceanDNA-b22995/target_genomes.txt --output OceanDNA-b22995/fastani_result.tsv --threads 1
[2023-03-17 05:32:09,143] [INFO] Task succeeded: fastANI
[2023-03-17 05:32:09,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:32:09,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:32:09,151] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:32:09,151] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:32:09,151] [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
Paludisphaera soli	strain=JC670	GCA_011064595.1	2712865	2712865	type	True	75.2053	56	759	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.0253	65	759	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.0031	62	759	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	74.9445	70	759	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	74.9223	61	759	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	74.8969	72	759	95	below_threshold
Azospirillum picis	strain=IMMIB TAR-3	GCA_017876115.1	488438	488438	type	True	74.8442	73	759	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.8086	62	759	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:32:09,151] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22995/tc_result.tsv
[2023-03-17 05:32:09,151] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:32:09,151] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:32:09,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/checkm_data
[2023-03-17 05:32:09,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:32:09,156] [INFO] Task started: CheckM
[2023-03-17 05:32:09,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22995/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22995/checkm_input OceanDNA-b22995/checkm_result
[2023-03-17 05:32:48,452] [INFO] Task succeeded: CheckM
[2023-03-17 05:32:48,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:32:48,457] [INFO] ===== Completeness check finished =====
[2023-03-17 05:32:48,457] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:32:48,457] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22995/markers.fasta)
[2023-03-17 05:32:48,458] [INFO] Task started: Blastn
[2023-03-17 05:32:48,458] [INFO] Running command: blastn -query OceanDNA-b22995/markers.fasta -db /var/lib/cwl/stgef8d5ee2-94e3-4c15-ad2b-2c4d88cc28b3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22995/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:32:49,278] [INFO] Task succeeded: Blastn
[2023-03-17 05:32:49,279] [INFO] Selected 23 target genomes.
[2023-03-17 05:32:49,279] [INFO] Target genome list was writen to OceanDNA-b22995/target_genomes_gtdb.txt
[2023-03-17 05:32:49,293] [INFO] Task started: fastANI
[2023-03-17 05:32:49,293] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c995f46-8074-47d7-8677-ada7796e1234/OceanDNA-b22995.fa --refList OceanDNA-b22995/target_genomes_gtdb.txt --output OceanDNA-b22995/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:33:05,638] [INFO] Task succeeded: fastANI
[2023-03-17 05:33:05,647] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:33:05,647] [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_011525785.1	s__WYBT01 sp011525785	75.8938	86	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__WYBT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709875.1	s__JADJLZ01 sp016709875	75.7905	74	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJLZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686265.1	s__GCA-2686265 sp002686265	75.7535	59	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2686265	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016712565.1	s__JADJQU01 sp016712565	75.6486	70	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JADJQU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007750655.1	s__Pla163 sp007750655	75.5749	75	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__Pla163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016779205.1	s__GCA-2862085 sp016779205	75.4891	59	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__GCA-2862085	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795205.1	s__JAEUHZ01 sp016795205	75.3548	76	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__JAEUHZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794425.1	s__JAEUHS01 sp016794425	75.3409	94	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902826945.1	s__RBC036 sp902826945	75.245	110	759	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA1135;f__GCA-002686595;g__RBC036	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003119115.1	s__Azospirillum sp003119115	74.961	64	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	97.55	95.10	0.94	0.88	3	-
GCF_008365375.1	s__Azospirillum sp008365375	74.7923	59	759	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 05:33:05,647] [INFO] GTDB search result was written to OceanDNA-b22995/result_gtdb.tsv
[2023-03-17 05:33:05,647] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:33:05,649] [INFO] DFAST_QC result json was written to OceanDNA-b22995/dqc_result.json
[2023-03-17 05:33:05,649] [INFO] DFAST_QC completed!
[2023-03-17 05:33:05,649] [INFO] Total running time: 0h1m35s