[2024-01-24 14:03:02,455] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:03:02,457] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:03:02,457] [INFO] DQC Reference Directory: /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference
[2024-01-24 14:03:03,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:03:03,738] [INFO] Task started: Prodigal
[2024-01-24 14:03:03,738] [INFO] Running command: gunzip -c /var/lib/cwl/stg5bd5ee66-5744-47e4-aba0-1a012106c238/GCF_009768975.1_ASM976897v1_genomic.fna.gz | prodigal -d GCF_009768975.1_ASM976897v1_genomic.fna/cds.fna -a GCF_009768975.1_ASM976897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:03:14,883] [INFO] Task succeeded: Prodigal
[2024-01-24 14:03:14,884] [INFO] Task started: HMMsearch
[2024-01-24 14:03:14,884] [INFO] Running command: hmmsearch --tblout GCF_009768975.1_ASM976897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/reference_markers.hmm GCF_009768975.1_ASM976897v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:03:15,169] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:03:15,170] [INFO] Found 6/6 markers.
[2024-01-24 14:03:15,212] [INFO] Query marker FASTA was written to GCF_009768975.1_ASM976897v1_genomic.fna/markers.fasta
[2024-01-24 14:03:15,212] [INFO] Task started: Blastn
[2024-01-24 14:03:15,212] [INFO] Running command: blastn -query GCF_009768975.1_ASM976897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/reference_markers.fasta -out GCF_009768975.1_ASM976897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:03:15,990] [INFO] Task succeeded: Blastn
[2024-01-24 14:03:15,993] [INFO] Selected 18 target genomes.
[2024-01-24 14:03:15,994] [INFO] Target genome list was writen to GCF_009768975.1_ASM976897v1_genomic.fna/target_genomes.txt
[2024-01-24 14:03:16,002] [INFO] Task started: fastANI
[2024-01-24 14:03:16,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd5ee66-5744-47e4-aba0-1a012106c238/GCF_009768975.1_ASM976897v1_genomic.fna.gz --refList GCF_009768975.1_ASM976897v1_genomic.fna/target_genomes.txt --output GCF_009768975.1_ASM976897v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:03:26,597] [INFO] Task succeeded: fastANI
[2024-01-24 14:03:26,598] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:03:26,598] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:03:26,617] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:03:26,618] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:03:26,618] [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 lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	100.0	1152	1152	95	conclusive
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	85.5293	843	1152	95	below_threshold
Sphingorhabdus profundilacus	strain=IMCC26285	GCA_009769755.1	2509718	2509718	type	True	84.9602	650	1152	95	below_threshold
Sphingorhabdus rigui	strain=DSM 29050	GCA_014196595.1	1282858	1282858	type	True	78.6932	366	1152	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	78.5243	294	1152	95	below_threshold
Sphingorhabdus wooponensis	strain=03SU3-P	GCA_003933235.1	940136	940136	type	True	78.4399	302	1152	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.2935	124	1152	95	below_threshold
Altererythrobacter lutimaris	strain=JGD-16	GCA_013371495.1	2743979	2743979	type	True	77.1685	76	1152	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.1144	128	1152	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	77.0908	92	1152	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.054	167	1152	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	76.7247	106	1152	95	below_threshold
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	76.5812	133	1152	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	76.5663	116	1152	95	below_threshold
Altericroceibacterium indicum	strain=DSM 18604	GCA_009828105.1	374177	374177	type	True	76.5553	75	1152	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.5542	127	1152	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	76.4941	118	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:03:26,620] [INFO] DFAST Taxonomy check result was written to GCF_009768975.1_ASM976897v1_genomic.fna/tc_result.tsv
[2024-01-24 14:03:26,622] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:03:26,622] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:03:26,622] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/checkm_data
[2024-01-24 14:03:26,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:03:26,667] [INFO] Task started: CheckM
[2024-01-24 14:03:26,667] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009768975.1_ASM976897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009768975.1_ASM976897v1_genomic.fna/checkm_input GCF_009768975.1_ASM976897v1_genomic.fna/checkm_result
[2024-01-24 14:04:03,136] [INFO] Task succeeded: CheckM
[2024-01-24 14:04:03,137] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:04:03,160] [INFO] ===== Completeness check finished =====
[2024-01-24 14:04:03,160] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:04:03,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009768975.1_ASM976897v1_genomic.fna/markers.fasta)
[2024-01-24 14:04:03,162] [INFO] Task started: Blastn
[2024-01-24 14:04:03,162] [INFO] Running command: blastn -query GCF_009768975.1_ASM976897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9dc76be4-68b5-4b33-b724-21a3d86d6edf/dqc_reference/reference_markers_gtdb.fasta -out GCF_009768975.1_ASM976897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:04:04,524] [INFO] Task succeeded: Blastn
[2024-01-24 14:04:04,528] [INFO] Selected 12 target genomes.
[2024-01-24 14:04:04,529] [INFO] Target genome list was writen to GCF_009768975.1_ASM976897v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:04:04,539] [INFO] Task started: fastANI
[2024-01-24 14:04:04,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg5bd5ee66-5744-47e4-aba0-1a012106c238/GCF_009768975.1_ASM976897v1_genomic.fna.gz --refList GCF_009768975.1_ASM976897v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009768975.1_ASM976897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:04:12,756] [INFO] Task succeeded: fastANI
[2024-01-24 14:04:12,773] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:04:12,774] [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_009768975.1	s__Sphingorhabdus_B lacus	100.0	1152	1152	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
GCA_013823985.1	s__Sphingorhabdus_B sp013823985	87.5982	862	1152	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_007280415.1	s__Sphingorhabdus_B contaminans	85.5162	844	1152	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	84.9763	649	1152	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	78.8514	394	1152	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_002282385.1	s__Sphingorhabdus_B sp002282385	78.8309	363	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.98	99.95	0.99	0.98	4	-
GCA_001464315.1	s__Sphingorhabdus_B sp001464315	78.7916	401	1152	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_002278855.1	s__Sphingorhabdus_B sp002278855	78.4337	326	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.65	99.65	0.97	0.97	2	-
GCA_002299195.1	s__Sphingorhabdus_B sp002299195	78.2733	286	1152	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_903821685.1	s__Sphingorhabdus_B sp903821685	78.0043	268	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingorhabdus_B	95.0	99.60	99.60	0.86	0.86	2	-
GCA_017987825.1	s__Sphingorhabdus_B sp017987825	77.7563	193	1152	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_003431825.1	s__Blastomonas fulva	77.1268	170	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Blastomonas	95.0	98.01	97.97	0.88	0.85	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:04:12,776] [INFO] GTDB search result was written to GCF_009768975.1_ASM976897v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:04:12,777] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:04:12,783] [INFO] DFAST_QC result json was written to GCF_009768975.1_ASM976897v1_genomic.fna/dqc_result.json
[2024-01-24 14:04:12,783] [INFO] DFAST_QC completed!
[2024-01-24 14:04:12,783] [INFO] Total running time: 0h1m10s