[2023-07-01 06:19:26,231] [INFO] DFAST_QC pipeline started.
[2023-07-01 06:19:26,234] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 06:19:26,234] [INFO] DQC Reference Directory: /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference
[2023-07-01 06:19:28,111] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 06:19:28,112] [INFO] Task started: Prodigal
[2023-07-01 06:19:28,113] [INFO] Running command: gunzip -c /var/lib/cwl/stgb26522a5-1aee-4749-9864-0a1b9475a92f/GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna.gz | prodigal -d GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/cds.fna -a GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 06:19:32,046] [INFO] Task succeeded: Prodigal
[2023-07-01 06:19:32,046] [INFO] Task started: HMMsearch
[2023-07-01 06:19:32,046] [INFO] Running command: hmmsearch --tblout GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/reference_markers.hmm GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/protein.faa > /dev/null
[2023-07-01 06:19:32,337] [INFO] Task succeeded: HMMsearch
[2023-07-01 06:19:32,338] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgb26522a5-1aee-4749-9864-0a1b9475a92f/GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna.gz]
[2023-07-01 06:19:32,373] [INFO] Query marker FASTA was written to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/markers.fasta
[2023-07-01 06:19:32,373] [INFO] Task started: Blastn
[2023-07-01 06:19:32,374] [INFO] Running command: blastn -query GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/reference_markers.fasta -out GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:19:33,006] [INFO] Task succeeded: Blastn
[2023-07-01 06:19:33,014] [INFO] Selected 14 target genomes.
[2023-07-01 06:19:33,014] [INFO] Target genome list was writen to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/target_genomes.txt
[2023-07-01 06:19:33,021] [INFO] Task started: fastANI
[2023-07-01 06:19:33,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26522a5-1aee-4749-9864-0a1b9475a92f/GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna.gz --refList GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/target_genomes.txt --output GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 06:19:40,983] [INFO] Task succeeded: fastANI
[2023-07-01 06:19:40,984] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 06:19:40,984] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 06:19:41,001] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 06:19:41,002] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 06:19:41,002] [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
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	77.4629	129	430	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	77.391	135	430	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	77.3884	132	430	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	77.3823	133	430	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	77.3469	134	430	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	77.2048	125	430	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	77.0583	110	430	95	below_threshold
Polaribacter atrinae	strain=KACC 17473	GCA_001640115.1	1333662	1333662	type	True	77.0421	114	430	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.9501	136	430	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.8399	136	430	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.7865	123	430	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.7192	116	430	95	below_threshold
Polaribacter cellanae	strain=SM13	GCA_017569185.1	2818493	2818493	type	True	76.7095	124	430	95	below_threshold
Polaribacter batillariae	strain=G4M1	GCA_017498485.1	2808900	2808900	type	True	76.6452	109	430	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 06:19:41,004] [INFO] DFAST Taxonomy check result was written to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/tc_result.tsv
[2023-07-01 06:19:41,005] [INFO] ===== Taxonomy check completed =====
[2023-07-01 06:19:41,005] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 06:19:41,005] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/checkm_data
[2023-07-01 06:19:41,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 06:19:41,040] [INFO] Task started: CheckM
[2023-07-01 06:19:41,041] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/checkm_input GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/checkm_result
[2023-07-01 06:20:00,363] [INFO] Task succeeded: CheckM
[2023-07-01 06:20:00,364] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 06:20:00,392] [INFO] ===== Completeness check finished =====
[2023-07-01 06:20:00,392] [INFO] ===== Start GTDB Search =====
[2023-07-01 06:20:00,392] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/markers.fasta)
[2023-07-01 06:20:00,393] [INFO] Task started: Blastn
[2023-07-01 06:20:00,393] [INFO] Running command: blastn -query GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/markers.fasta -db /var/lib/cwl/stg25a245cc-0968-4964-ad0c-83daa5310fae/dqc_reference/reference_markers_gtdb.fasta -out GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 06:20:01,344] [INFO] Task succeeded: Blastn
[2023-07-01 06:20:01,349] [INFO] Selected 10 target genomes.
[2023-07-01 06:20:01,350] [INFO] Target genome list was writen to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 06:20:01,359] [INFO] Task started: fastANI
[2023-07-01 06:20:01,359] [INFO] Running command: fastANI --query /var/lib/cwl/stgb26522a5-1aee-4749-9864-0a1b9475a92f/GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna.gz --refList GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/target_genomes_gtdb.txt --output GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 06:20:06,374] [INFO] Task succeeded: fastANI
[2023-07-01 06:20:06,392] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 06:20:06,393] [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_018608485.1	s__SCGC-AAA160-P02 sp018608485	99.2387	347	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	99.40	99.40	0.78	0.78	2	conclusive
GCA_015665265.1	s__SCGC-AAA160-P02 sp015665265	93.6332	384	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.43	96.43	0.88	0.88	2	-
GCA_905479435.1	s__SCGC-AAA160-P02 sp905479435	83.1985	245	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000383355.1	s__SCGC-AAA160-P02 sp000383355	81.6755	309	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__SCGC-AAA160-P02	95.0	96.64	95.28	0.86	0.84	6	-
GCF_001975665.1	s__Polaribacter reichenbachii	77.3884	132	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_018861005.1	s__Polaribacter vadi_A	77.2834	144	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163835.1	s__Polaribacter sp002163835	77.1233	142	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001640115.1	s__Polaribacter atrinae	77.0421	114	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105985.1	s__Tenacibaculum sp900105985	76.6384	104	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	98.69	98.69	0.93	0.93	2	-
GCF_012524075.1	s__Lutibacter sp012524075	76.2278	71	430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 06:20:06,395] [INFO] GTDB search result was written to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/result_gtdb.tsv
[2023-07-01 06:20:06,396] [INFO] ===== GTDB Search completed =====
[2023-07-01 06:20:06,400] [INFO] DFAST_QC result json was written to GCA_943845665.1_20200506_Bin_Bin_232_sub_2-contigs.fa_genomic.fna/dqc_result.json
[2023-07-01 06:20:06,401] [INFO] DFAST_QC completed!
[2023-07-01 06:20:06,401] [INFO] Total running time: 0h0m40s