[2023-06-27 08:16:01,681] [INFO] DFAST_QC pipeline started.
[2023-06-27 08:16:01,712] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 08:16:01,712] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference
[2023-06-27 08:16:03,880] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 08:16:03,880] [INFO] Task started: Prodigal
[2023-06-27 08:16:03,881] [INFO] Running command: gunzip -c /var/lib/cwl/stgc4660b4e-7294-44f3-b787-da02b2838cd9/GCA_002291855.1_ASM229185v1_genomic.fna.gz | prodigal -d GCA_002291855.1_ASM229185v1_genomic.fna/cds.fna -a GCA_002291855.1_ASM229185v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 08:16:09,728] [INFO] Task succeeded: Prodigal
[2023-06-27 08:16:09,729] [INFO] Task started: HMMsearch
[2023-06-27 08:16:09,729] [INFO] Running command: hmmsearch --tblout GCA_002291855.1_ASM229185v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/reference_markers.hmm GCA_002291855.1_ASM229185v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 08:16:09,962] [INFO] Task succeeded: HMMsearch
[2023-06-27 08:16:09,964] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc4660b4e-7294-44f3-b787-da02b2838cd9/GCA_002291855.1_ASM229185v1_genomic.fna.gz]
[2023-06-27 08:16:09,991] [INFO] Query marker FASTA was written to GCA_002291855.1_ASM229185v1_genomic.fna/markers.fasta
[2023-06-27 08:16:09,992] [INFO] Task started: Blastn
[2023-06-27 08:16:09,992] [INFO] Running command: blastn -query GCA_002291855.1_ASM229185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/reference_markers.fasta -out GCA_002291855.1_ASM229185v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:16:10,876] [INFO] Task succeeded: Blastn
[2023-06-27 08:16:10,881] [INFO] Selected 14 target genomes.
[2023-06-27 08:16:10,882] [INFO] Target genome list was writen to GCA_002291855.1_ASM229185v1_genomic.fna/target_genomes.txt
[2023-06-27 08:16:10,884] [INFO] Task started: fastANI
[2023-06-27 08:16:10,884] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4660b4e-7294-44f3-b787-da02b2838cd9/GCA_002291855.1_ASM229185v1_genomic.fna.gz --refList GCA_002291855.1_ASM229185v1_genomic.fna/target_genomes.txt --output GCA_002291855.1_ASM229185v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 08:16:20,463] [INFO] Task succeeded: fastANI
[2023-06-27 08:16:20,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 08:16:20,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 08:16:20,479] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 08:16:20,480] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 08:16:20,480] [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
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	91.7803	612	673	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	80.2138	365	673	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	80.0056	342	673	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	79.1525	336	673	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	78.8845	304	673	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.7224	313	673	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.6797	314	673	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	78.5881	268	673	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.5217	305	673	95	below_threshold
Sphingobium jiangsuense	strain=DSM 26189	GCA_014196495.1	870476	870476	type	True	78.4872	318	673	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.3441	303	673	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	78.3037	275	673	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	78.2949	275	673	95	below_threshold
Sphingomonas sinipercae	strain=HDW15C	GCA_011302055.1	2714944	2714944	type	True	77.5307	172	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 08:16:20,483] [INFO] DFAST Taxonomy check result was written to GCA_002291855.1_ASM229185v1_genomic.fna/tc_result.tsv
[2023-06-27 08:16:20,484] [INFO] ===== Taxonomy check completed =====
[2023-06-27 08:16:20,484] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 08:16:20,484] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/checkm_data
[2023-06-27 08:16:20,485] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 08:16:20,515] [INFO] Task started: CheckM
[2023-06-27 08:16:20,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002291855.1_ASM229185v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002291855.1_ASM229185v1_genomic.fna/checkm_input GCA_002291855.1_ASM229185v1_genomic.fna/checkm_result
[2023-06-27 08:16:43,360] [INFO] Task succeeded: CheckM
[2023-06-27 08:16:43,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.19%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 08:16:43,384] [INFO] ===== Completeness check finished =====
[2023-06-27 08:16:43,384] [INFO] ===== Start GTDB Search =====
[2023-06-27 08:16:43,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002291855.1_ASM229185v1_genomic.fna/markers.fasta)
[2023-06-27 08:16:43,385] [INFO] Task started: Blastn
[2023-06-27 08:16:43,385] [INFO] Running command: blastn -query GCA_002291855.1_ASM229185v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbfcc1382-ffc9-4320-96c1-9a39351a9459/dqc_reference/reference_markers_gtdb.fasta -out GCA_002291855.1_ASM229185v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 08:16:45,007] [INFO] Task succeeded: Blastn
[2023-06-27 08:16:45,012] [INFO] Selected 13 target genomes.
[2023-06-27 08:16:45,012] [INFO] Target genome list was writen to GCA_002291855.1_ASM229185v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 08:16:45,024] [INFO] Task started: fastANI
[2023-06-27 08:16:45,024] [INFO] Running command: fastANI --query /var/lib/cwl/stgc4660b4e-7294-44f3-b787-da02b2838cd9/GCA_002291855.1_ASM229185v1_genomic.fna.gz --refList GCA_002291855.1_ASM229185v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002291855.1_ASM229185v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 08:16:54,018] [INFO] Task succeeded: fastANI
[2023-06-27 08:16:54,041] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 08:16:54,042] [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_002291855.1	s__Sphingomonas_B sp002291855	100.0	658	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009913435.1	s__Sphingomonas_B sp009913435	91.7803	612	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009753715.1	s__Sphingomonas_B horti	80.2277	364	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	80.0057	342	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013044515.1	s__Sphingomonas_B sp013044515	79.8895	358	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.8595	322	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240865.1	s__Sphingomonas_B sp018240865	79.8115	344	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	79.1805	334	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.1757	324	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_001598455.1	s__Sphingomonas pruni	78.618	266	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013344685.1	s__Sphingomonas sp013344685	78.5644	324	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196495.1	s__Sphingobium jiangsuense	78.478	319	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	78.4511	310	673	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 08:16:54,044] [INFO] GTDB search result was written to GCA_002291855.1_ASM229185v1_genomic.fna/result_gtdb.tsv
[2023-06-27 08:16:54,044] [INFO] ===== GTDB Search completed =====
[2023-06-27 08:16:54,055] [INFO] DFAST_QC result json was written to GCA_002291855.1_ASM229185v1_genomic.fna/dqc_result.json
[2023-06-27 08:16:54,056] [INFO] DFAST_QC completed!
[2023-06-27 08:16:54,056] [INFO] Total running time: 0h0m52s