[2024-01-24 11:26:19,470] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:19,472] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:19,472] [INFO] DQC Reference Directory: /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference
[2024-01-24 11:26:20,704] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:20,705] [INFO] Task started: Prodigal
[2024-01-24 11:26:20,705] [INFO] Running command: gunzip -c /var/lib/cwl/stgae1e9e68-6fb7-4cae-b9be-7b00603ec017/GCF_007280415.1_ASM728041v1_genomic.fna.gz | prodigal -d GCF_007280415.1_ASM728041v1_genomic.fna/cds.fna -a GCF_007280415.1_ASM728041v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:31,489] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:31,490] [INFO] Task started: HMMsearch
[2024-01-24 11:26:31,490] [INFO] Running command: hmmsearch --tblout GCF_007280415.1_ASM728041v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/reference_markers.hmm GCF_007280415.1_ASM728041v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:31,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:31,783] [INFO] Found 6/6 markers.
[2024-01-24 11:26:31,811] [INFO] Query marker FASTA was written to GCF_007280415.1_ASM728041v1_genomic.fna/markers.fasta
[2024-01-24 11:26:31,812] [INFO] Task started: Blastn
[2024-01-24 11:26:31,812] [INFO] Running command: blastn -query GCF_007280415.1_ASM728041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/reference_markers.fasta -out GCF_007280415.1_ASM728041v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:32,578] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:32,582] [INFO] Selected 18 target genomes.
[2024-01-24 11:26:32,583] [INFO] Target genome list was writen to GCF_007280415.1_ASM728041v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:32,596] [INFO] Task started: fastANI
[2024-01-24 11:26:32,596] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1e9e68-6fb7-4cae-b9be-7b00603ec017/GCF_007280415.1_ASM728041v1_genomic.fna.gz --refList GCF_007280415.1_ASM728041v1_genomic.fna/target_genomes.txt --output GCF_007280415.1_ASM728041v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:43,691] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:43,691] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:43,691] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:43,704] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:43,705] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:43,705] [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
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	100.0	1096	1096	95	conclusive
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	85.5824	845	1096	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	82.3368	605	1096	95	below_threshold
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	78.5627	260	1096	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	78.4376	337	1096	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	77.7778	248	1096	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	77.3528	153	1096	95	below_threshold
Sphingobium baderi	strain=LL03	GCA_001046655.1	1332080	1332080	type	True	77.2792	130	1096	95	below_threshold
Stakelama sediminis	strain=DSM 27203	GCA_014199335.1	463200	463200	type	True	77.0487	126	1096	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	76.8102	106	1096	95	below_threshold
Qipengyuania gelatinilytica	strain=1NDH1	GCA_019711315.1	2867231	2867231	type	True	76.688	104	1096	95	below_threshold
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	76.6288	158	1096	95	below_threshold
Novosphingobium profundi	strain=F72	GCA_018491765.1	1774954	1774954	type	True	76.5906	69	1096	95	below_threshold
Qipengyuania polymorpha	strain=1NDH17	GCA_019711435.1	2867234	2867234	type	True	76.5712	110	1096	95	below_threshold
Croceicoccus sediminis	strain=S2-4-2	GCA_007570835.1	2571150	2571150	type	True	76.5	95	1096	95	below_threshold
Sphingorhabdus lutea	strain=LPB0140	GCA_001889025.1	1913578	1913578	type	True	76.4294	57	1096	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	76.3598	97	1096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:43,706] [INFO] DFAST Taxonomy check result was written to GCF_007280415.1_ASM728041v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:43,707] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:43,707] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:43,707] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/checkm_data
[2024-01-24 11:26:43,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:43,741] [INFO] Task started: CheckM
[2024-01-24 11:26:43,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007280415.1_ASM728041v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007280415.1_ASM728041v1_genomic.fna/checkm_input GCF_007280415.1_ASM728041v1_genomic.fna/checkm_result
[2024-01-24 11:27:19,039] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:19,041] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:19,062] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:19,062] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:19,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007280415.1_ASM728041v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:19,063] [INFO] Task started: Blastn
[2024-01-24 11:27:19,063] [INFO] Running command: blastn -query GCF_007280415.1_ASM728041v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1e0862c2-1ccf-4611-b3fb-122df67be0c6/dqc_reference/reference_markers_gtdb.fasta -out GCF_007280415.1_ASM728041v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:20,403] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:20,407] [INFO] Selected 15 target genomes.
[2024-01-24 11:27:20,407] [INFO] Target genome list was writen to GCF_007280415.1_ASM728041v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:20,441] [INFO] Task started: fastANI
[2024-01-24 11:27:20,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1e9e68-6fb7-4cae-b9be-7b00603ec017/GCF_007280415.1_ASM728041v1_genomic.fna.gz --refList GCF_007280415.1_ASM728041v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007280415.1_ASM728041v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:30,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:30,350] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:30,351] [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_007280415.1	s__Sphingorhabdus_B contaminans	100.0	1096	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009768975.1	s__Sphingorhabdus_B lacus	85.5823	845	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823985.1	s__Sphingorhabdus_B sp013823985	84.3231	780	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769755.1	s__Sphingorhabdus_B profundilacus	82.3313	604	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016742125.1	s__Sphingorhabdus_B sp016742125	78.8286	377	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001464315.1	s__Sphingorhabdus_B sp001464315	78.4535	376	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196595.1	s__Sphingorhabdus_B rigui	78.4498	336	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002479765.1	s__Sphingorhabdus_B sp002479765	78.3615	331	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016707885.1	s__Sphingorhabdus_B sp016707885	78.2227	248	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002255985.1	s__Sphingorhabdus_B sp002255985	78.212	331	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.49	98.44	0.89	0.89	3	-
GCA_016462305.1	s__Sphingorhabdus_B sp016462305	78.2081	222	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	98.63	98.63	0.82	0.82	2	-
GCA_002299195.1	s__Sphingorhabdus_B sp002299195	78.1773	255	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	76.8202	157	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	76.7281	145	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018491765.1	s__Novosphingobium profundi	76.5598	70	1096	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:30,352] [INFO] GTDB search result was written to GCF_007280415.1_ASM728041v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:30,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:30,362] [INFO] DFAST_QC result json was written to GCF_007280415.1_ASM728041v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:30,362] [INFO] DFAST_QC completed!
[2024-01-24 11:27:30,362] [INFO] Total running time: 0h1m11s