[2024-01-24 13:09:51,812] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,815] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,815] [INFO] DQC Reference Directory: /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference
[2024-01-24 13:09:53,300] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:53,301] [INFO] Task started: Prodigal
[2024-01-24 13:09:53,301] [INFO] Running command: gunzip -c /var/lib/cwl/stg480a36e9-d3b2-4ab2-bc60-3750a898f140/GCF_004339765.1_ASM433976v1_genomic.fna.gz | prodigal -d GCF_004339765.1_ASM433976v1_genomic.fna/cds.fna -a GCF_004339765.1_ASM433976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:04,294] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:04,295] [INFO] Task started: HMMsearch
[2024-01-24 13:10:04,295] [INFO] Running command: hmmsearch --tblout GCF_004339765.1_ASM433976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/reference_markers.hmm GCF_004339765.1_ASM433976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:04,600] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:04,601] [INFO] Found 6/6 markers.
[2024-01-24 13:10:04,636] [INFO] Query marker FASTA was written to GCF_004339765.1_ASM433976v1_genomic.fna/markers.fasta
[2024-01-24 13:10:04,636] [INFO] Task started: Blastn
[2024-01-24 13:10:04,637] [INFO] Running command: blastn -query GCF_004339765.1_ASM433976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/reference_markers.fasta -out GCF_004339765.1_ASM433976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:05,258] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:05,261] [INFO] Selected 28 target genomes.
[2024-01-24 13:10:05,262] [INFO] Target genome list was writen to GCF_004339765.1_ASM433976v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:05,272] [INFO] Task started: fastANI
[2024-01-24 13:10:05,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg480a36e9-d3b2-4ab2-bc60-3750a898f140/GCF_004339765.1_ASM433976v1_genomic.fna.gz --refList GCF_004339765.1_ASM433976v1_genomic.fna/target_genomes.txt --output GCF_004339765.1_ASM433976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:26,664] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:26,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:26,665] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:26,678] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:26,678] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:26,679] [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
Albibacterium bauzanense	strain=DSM 22554	GCA_004339765.1	653929	653929	type	True	100.0	1024	1024	95	conclusive
Pedobacter indicus	strain=SM1810	GCA_003449035.1	2292082	2292082	type	True	78.4578	148	1024	95	below_threshold
Sphingobacterium hungaricum	strain=KB22	GCA_015210005.1	2082723	2082723	type	True	77.0287	59	1024	95	below_threshold
Olivibacter domesticus	strain=DSM 18733	GCA_900109575.1	407022	407022	type	True	76.8145	69	1024	95	below_threshold
Sphingobacterium rhinopitheci	strain=WQ 047	GCA_022627575.1	2781960	2781960	type	True	76.5938	51	1024	95	below_threshold
Pedobacter planticolens	strain=LMG 31464	GCA_014172375.1	2679964	2679964	type	True	76.4462	59	1024	95	below_threshold
Pedobacter cryophilus	strain=AR-3-17	GCA_005116455.1	2571271	2571271	type	True	76.4096	51	1024	95	below_threshold
Daejeonella rubra	strain=DSM 24536	GCA_900103545.1	990371	990371	type	True	76.3282	53	1024	95	below_threshold
Pedobacter chinensis	strain=JDX94	GCA_003339865.1	2282421	2282421	type	True	76.313	51	1024	95	below_threshold
Pedobacter hiemivivus	strain=RP-3-8	GCA_004331685.1	2530454	2530454	type	True	76.244	51	1024	95	below_threshold
Pedobacter polaris	strain=RP-3-22	GCA_005116505.1	2571273	2571273	type	True	76.162	54	1024	95	below_threshold
Sphingobacterium faecium	strain=NBRC 15299	GCA_007990875.1	34087	34087	type	True	76.0244	60	1024	95	below_threshold
Sphingobacterium puteale	strain=M05W1-28	GCA_003627955.1	2420510	2420510	type	True	75.9025	51	1024	95	below_threshold
Pedobacter panaciterrae	strain=LMG 23400	GCA_013204795.1	363849	363849	type	True	75.8864	63	1024	95	below_threshold
Arcticibacter svalbardensis	strain=MN12-7	GCA_000403135.1	1288027	1288027	type	True	75.8175	50	1024	95	below_threshold
Pedobacter foliorum	strain=LMG 31463	GCA_013266735.1	2739058	2739058	type	True	75.673	65	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:26,680] [INFO] DFAST Taxonomy check result was written to GCF_004339765.1_ASM433976v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:26,681] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:26,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:26,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/checkm_data
[2024-01-24 13:10:26,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:26,715] [INFO] Task started: CheckM
[2024-01-24 13:10:26,715] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339765.1_ASM433976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339765.1_ASM433976v1_genomic.fna/checkm_input GCF_004339765.1_ASM433976v1_genomic.fna/checkm_result
[2024-01-24 13:11:02,466] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:02,468] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:02,489] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:02,489] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:02,490] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339765.1_ASM433976v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:02,490] [INFO] Task started: Blastn
[2024-01-24 13:11:02,490] [INFO] Running command: blastn -query GCF_004339765.1_ASM433976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf3c32599-9b17-447d-8654-84e5f5884606/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339765.1_ASM433976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:03,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:03,253] [INFO] Selected 27 target genomes.
[2024-01-24 13:11:03,254] [INFO] Target genome list was writen to GCF_004339765.1_ASM433976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:03,275] [INFO] Task started: fastANI
[2024-01-24 13:11:03,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg480a36e9-d3b2-4ab2-bc60-3750a898f140/GCF_004339765.1_ASM433976v1_genomic.fna.gz --refList GCF_004339765.1_ASM433976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339765.1_ASM433976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:23,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:23,469] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:11:23,470] [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_004339765.1	s__Albibacterium bauzanense	100.0	1023	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Albibacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003449035.1	s__Albibacterium indicum	78.3912	148	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Albibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000192845.1	s__Pseudosphingobacterium jilunii	77.3821	63	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	98.40	98.36	0.86	0.86	3	-
GCF_000747525.1	s__Sphingobacterium sp000747525	77.3755	69	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015210005.1	s__Sphingobacterium sp015210005	77.0683	58	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002736205.1	s__Pedobacter ginsengisoli	76.9764	70	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004368405.1	s__Pseudosphingobacterium sp004368405	76.9332	55	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109575.1	s__Pseudosphingobacterium domesticum	76.791	68	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pseudosphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014172375.1	s__Pedobacter planticolens	76.4462	59	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116455.1	s__Pelobium sp005116455	76.4096	51	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pelobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103545.1	s__Daejeonella rubra	76.2917	54	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Daejeonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048855.1	s__Sphingobacterium olei	76.2492	53	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Sphingobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005116505.1	s__Pedobacter sp005116505	76.162	54	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018492665.1	s__Pedobacter sp018492665	76.1206	59	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054115.1	s__Pedobacter sp003054115	76.0263	64	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000403135.1	s__Arcticibacter svalbardensis	75.8175	50	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Arcticibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013266735.1	s__Pedobacter foliorum	75.673	65	1024	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Pedobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:23,471] [INFO] GTDB search result was written to GCF_004339765.1_ASM433976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:23,472] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:23,476] [INFO] DFAST_QC result json was written to GCF_004339765.1_ASM433976v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:23,476] [INFO] DFAST_QC completed!
[2024-01-24 13:11:23,476] [INFO] Total running time: 0h1m32s