[2023-06-19 13:14:19,795] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:14:19,797] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:14:19,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference
[2023-06-19 13:14:21,129] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:14:21,130] [INFO] Task started: Prodigal
[2023-06-19 13:14:21,131] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a6a2e07-a2ac-4839-935b-345e8e4a5a53/GCA_013002005.1_ASM1300200v1_genomic.fna.gz | prodigal -d GCA_013002005.1_ASM1300200v1_genomic.fna/cds.fna -a GCA_013002005.1_ASM1300200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:14:30,391] [INFO] Task succeeded: Prodigal
[2023-06-19 13:14:30,392] [INFO] Task started: HMMsearch
[2023-06-19 13:14:30,392] [INFO] Running command: hmmsearch --tblout GCA_013002005.1_ASM1300200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/reference_markers.hmm GCA_013002005.1_ASM1300200v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:14:30,644] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:14:30,645] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a6a2e07-a2ac-4839-935b-345e8e4a5a53/GCA_013002005.1_ASM1300200v1_genomic.fna.gz]
[2023-06-19 13:14:30,677] [INFO] Query marker FASTA was written to GCA_013002005.1_ASM1300200v1_genomic.fna/markers.fasta
[2023-06-19 13:14:30,678] [INFO] Task started: Blastn
[2023-06-19 13:14:30,678] [INFO] Running command: blastn -query GCA_013002005.1_ASM1300200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/reference_markers.fasta -out GCA_013002005.1_ASM1300200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:14:31,271] [INFO] Task succeeded: Blastn
[2023-06-19 13:14:31,275] [INFO] Selected 24 target genomes.
[2023-06-19 13:14:31,276] [INFO] Target genome list was writen to GCA_013002005.1_ASM1300200v1_genomic.fna/target_genomes.txt
[2023-06-19 13:14:31,281] [INFO] Task started: fastANI
[2023-06-19 13:14:31,282] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6a2e07-a2ac-4839-935b-345e8e4a5a53/GCA_013002005.1_ASM1300200v1_genomic.fna.gz --refList GCA_013002005.1_ASM1300200v1_genomic.fna/target_genomes.txt --output GCA_013002005.1_ASM1300200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:14:45,968] [INFO] Task succeeded: fastANI
[2023-06-19 13:14:45,968] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:14:45,968] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:14:45,986] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:14:45,986] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:14:45,987] [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
Eudoraea adriatica	strain=DSM 19308	GCA_000382125.1	446681	446681	type	True	77.7502	99	620	95	below_threshold
Muriicola soli	strain=MMS17-SY002	GCA_004139715.1	2507538	2507538	type	True	77.173	110	620	95	below_threshold
Arenibacter arenosicollis	strain=BSSL-BM3	GCA_014397245.1	2762274	2762274	type	True	76.8553	50	620	95	below_threshold
Arenibacter troitsensis	strain=DSM 19835	GCA_900177645.1	188872	188872	type	True	76.7377	53	620	95	below_threshold
Maribacter orientalis	strain=DSM 16471	GCA_900109345.1	228957	228957	type	True	76.6945	59	620	95	below_threshold
Maribacter litoralis	strain=SDRB-Phe2	GCA_003075045.1	2059726	2059726	type	True	76.6709	63	620	95	below_threshold
Cellulophaga baltica	strain=DSM 24729	GCA_900102165.1	76594	76594	type	True	76.6643	56	620	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	76.6471	69	620	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001673755.1	1836467	1836467	type	True	76.6039	65	620	95	below_threshold
Maribacter hydrothermalis	strain=T28	GCA_001913155.1	1836467	1836467	type	True	76.5998	64	620	95	below_threshold
Maribacter polysiphoniae	strain=KCTC 22021	GCA_014673435.1	429344	429344	type	True	76.5139	55	620	95	below_threshold
Maribacter luteus	strain=RZ05	GCA_009674825.1	2594478	2594478	type	True	76.5015	51	620	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.4519	56	620	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.2886	59	620	95	below_threshold
Arenibacter algicola	strain=TG409	GCA_000733925.1	616991	616991	type	True	76.1627	69	620	95	below_threshold
Arenibacter echinorum	strain=DSM 23522	GCA_003259375.1	440515	440515	type	True	76.1254	58	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:14:45,990] [INFO] DFAST Taxonomy check result was written to GCA_013002005.1_ASM1300200v1_genomic.fna/tc_result.tsv
[2023-06-19 13:14:45,991] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:14:45,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:14:45,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/checkm_data
[2023-06-19 13:14:45,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:14:46,023] [INFO] Task started: CheckM
[2023-06-19 13:14:46,023] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013002005.1_ASM1300200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013002005.1_ASM1300200v1_genomic.fna/checkm_input GCA_013002005.1_ASM1300200v1_genomic.fna/checkm_result
[2023-06-19 13:15:17,443] [INFO] Task succeeded: CheckM
[2023-06-19 13:15:17,445] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 13:15:17,472] [INFO] ===== Completeness check finished =====
[2023-06-19 13:15:17,472] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:15:17,473] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013002005.1_ASM1300200v1_genomic.fna/markers.fasta)
[2023-06-19 13:15:17,473] [INFO] Task started: Blastn
[2023-06-19 13:15:17,474] [INFO] Running command: blastn -query GCA_013002005.1_ASM1300200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg57845b29-a0e4-4527-bb4d-465c682399ef/dqc_reference/reference_markers_gtdb.fasta -out GCA_013002005.1_ASM1300200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:15:18,239] [INFO] Task succeeded: Blastn
[2023-06-19 13:15:18,244] [INFO] Selected 23 target genomes.
[2023-06-19 13:15:18,244] [INFO] Target genome list was writen to GCA_013002005.1_ASM1300200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:15:18,269] [INFO] Task started: fastANI
[2023-06-19 13:15:18,269] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a6a2e07-a2ac-4839-935b-345e8e4a5a53/GCA_013002005.1_ASM1300200v1_genomic.fna.gz --refList GCA_013002005.1_ASM1300200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013002005.1_ASM1300200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:15:31,547] [INFO] Task succeeded: fastANI
[2023-06-19 13:15:31,567] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 13:15:31,567] [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_000382125.1	s__Eudoraea adriatica	77.784	98	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042315.1	s__Muriicola sp013042315	77.6268	71	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	99.31	99.31	0.85	0.85	2	-
GCF_004139715.1	s__Muriicola sp004139715	77.173	110	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479615.1	s__Eudoraea sp905479615	77.0265	59	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Eudoraea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013042255.1	s__Muriicola sp013042255	76.8614	62	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	98.63	98.55	0.78	0.75	6	-
GCF_900177645.1	s__Arenibacter troitsensis	76.7377	53	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102165.1	s__Cellulophaga baltica	76.6573	55	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	97.62	97.40	0.90	0.89	7	-
GCF_011927795.1	s__Saonia flava	76.6412	68	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	76.6338	60	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	76.6233	62	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010993855.1	s__Muricauda sp010993855	76.4983	66	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.4519	56	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_018860365.1	s__Arenibacter algicola_B	76.4103	65	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001430825.1	s__Sediminicola sp001430825	76.3985	72	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Sediminicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003201775.1	s__Arenibacter sp003201775	76.3247	57	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.2693	61	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744255.1	s__Maribacter_B sp016744255	76.2678	65	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000733925.1	s__Arenibacter algicola	76.1752	67	620	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	98.04	97.34	0.85	0.81	5	-
--------------------------------------------------------------------------------
[2023-06-19 13:15:31,569] [INFO] GTDB search result was written to GCA_013002005.1_ASM1300200v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:15:31,570] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:15:31,574] [INFO] DFAST_QC result json was written to GCA_013002005.1_ASM1300200v1_genomic.fna/dqc_result.json
[2023-06-19 13:15:31,574] [INFO] DFAST_QC completed!
[2023-06-19 13:15:31,574] [INFO] Total running time: 0h1m12s