[2024-01-24 15:26:50,746] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:50,753] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:50,753] [INFO] DQC Reference Directory: /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference
[2024-01-24 15:26:52,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:52,911] [INFO] Task started: Prodigal
[2024-01-24 15:26:52,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg76c6bb24-bb63-4ed8-91c3-d54020507ebc/GCF_026157035.1_ASM2615703v1_genomic.fna.gz | prodigal -d GCF_026157035.1_ASM2615703v1_genomic.fna/cds.fna -a GCF_026157035.1_ASM2615703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:59,351] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:59,352] [INFO] Task started: HMMsearch
[2024-01-24 15:26:59,352] [INFO] Running command: hmmsearch --tblout GCF_026157035.1_ASM2615703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/reference_markers.hmm GCF_026157035.1_ASM2615703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:59,617] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:59,618] [INFO] Found 6/6 markers.
[2024-01-24 15:26:59,639] [INFO] Query marker FASTA was written to GCF_026157035.1_ASM2615703v1_genomic.fna/markers.fasta
[2024-01-24 15:26:59,640] [INFO] Task started: Blastn
[2024-01-24 15:26:59,640] [INFO] Running command: blastn -query GCF_026157035.1_ASM2615703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/reference_markers.fasta -out GCF_026157035.1_ASM2615703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:00,882] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:00,888] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:00,888] [INFO] Target genome list was writen to GCF_026157035.1_ASM2615703v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:00,900] [INFO] Task started: fastANI
[2024-01-24 15:27:00,900] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c6bb24-bb63-4ed8-91c3-d54020507ebc/GCF_026157035.1_ASM2615703v1_genomic.fna.gz --refList GCF_026157035.1_ASM2615703v1_genomic.fna/target_genomes.txt --output GCF_026157035.1_ASM2615703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:09,904] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:09,905] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:09,905] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:09,918] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:09,918] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:09,919] [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
Sphingomicrobium astaxanthinifaciens	strain=JCM 18551	GCA_022865105.1	1227949	1227949	type	True	81.0351	493	754	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	80.9696	474	754	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	80.9476	493	754	95	below_threshold
Sphingomicrobium lutaoense	strain=DSM 24194	GCA_014195685.1	515949	515949	type	True	80.1403	422	754	95	below_threshold
Sphingomicrobium flavum	strain=JCM 18555	GCA_024721605.1	1229164	1229164	type	True	79.7038	414	754	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	79.4215	375	754	95	below_threshold
Sphingomonas ginkgonis	strain=HMF7854	GCA_003970925.1	2315330	2315330	type	True	79.2565	368	754	95	below_threshold
Sphingomonas mesophila	strain=SYSUP0001	GCA_003499275.1	2303576	2303576	type	True	79.1934	377	754	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	78.4978	274	754	95	below_threshold
Sphingomonas xanthus	strain=AE3	GCA_007998985.1	2594473	2594473	type	True	78.3823	278	754	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	78.0143	274	754	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	77.9044	259	754	95	below_threshold
Sphingomonas deserti	strain=GL-C-18	GCA_003012735.1	2116704	2116704	type	True	77.7894	282	754	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	77.6239	235	754	95	below_threshold
Parasphingopyxis algicola	strain=JCM 31719	GCA_013378075.1	2026624	2026624	type	True	77.5629	222	754	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.5137	271	754	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:09,920] [INFO] DFAST Taxonomy check result was written to GCF_026157035.1_ASM2615703v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:09,921] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:09,921] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:09,921] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/checkm_data
[2024-01-24 15:27:09,922] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:09,948] [INFO] Task started: CheckM
[2024-01-24 15:27:09,948] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026157035.1_ASM2615703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026157035.1_ASM2615703v1_genomic.fna/checkm_input GCF_026157035.1_ASM2615703v1_genomic.fna/checkm_result
[2024-01-24 15:27:34,504] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:34,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:34,528] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:34,529] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:34,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026157035.1_ASM2615703v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:34,529] [INFO] Task started: Blastn
[2024-01-24 15:27:34,529] [INFO] Running command: blastn -query GCF_026157035.1_ASM2615703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge54d8cc0-1939-4116-9824-3e8b377004ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_026157035.1_ASM2615703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:36,546] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:36,550] [INFO] Selected 24 target genomes.
[2024-01-24 15:27:36,551] [INFO] Target genome list was writen to GCF_026157035.1_ASM2615703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:36,576] [INFO] Task started: fastANI
[2024-01-24 15:27:36,576] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c6bb24-bb63-4ed8-91c3-d54020507ebc/GCF_026157035.1_ASM2615703v1_genomic.fna.gz --refList GCF_026157035.1_ASM2615703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026157035.1_ASM2615703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:52,145] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:52,164] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:27:52,164] [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_014195685.1	s__Sphingomicrobium lutaoense	80.1541	421	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000585415.1	s__Sphingomicrobium jaspsi	79.4215	375	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003970925.1	s__Sphingomicrobium sp003970925	79.2565	368	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363895.1	s__Sphingomicrobium ginsengisoli	79.2231	372	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003499275.1	s__Sphingomicrobium mesophila	79.2055	376	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001055.1	s__Sphingomicrobium sp004282935	79.1205	324	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	99.85	99.85	0.95	0.95	2	-
GCA_013816785.1	s__Sphingomicrobium sp013816785	78.6466	310	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489495.1	s__Sphingomicrobium daechungense	78.6191	245	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720245.1	s__Sphingomicrobium sp009720245	78.4784	286	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007998985.1	s__Sphingomicrobium xanthus	78.3964	277	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564275.1	s__Allosphingosinicella parva	78.341	315	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019247755.1	s__Sphingomicrobium sp019247755	78.3136	181	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016025255.1	s__Allosphingosinicella sp016025255	78.3086	243	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806285.1	s__Sphingomicrobium sp902806285	78.2639	259	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000383095.1	s__Sphingomonas_N sp000383095	78.2541	278	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019242355.1	s__Sphingomicrobium sp019242355	78.2145	239	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	78.1034	230	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144715.1	s__Sphingomonas sp005144715	78.0534	271	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019239915.1	s__Sphingomonas_N sp019239915	77.9806	247	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003347635.1	s__Allosphingosinicella sp003347635	77.9771	301	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902806275.1	s__Sphingomicrobium sp902806275	77.8123	185	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003012735.1	s__Allosphingosinicella deserti	77.778	283	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013378075.1	s__Parasphingopyxis algicola	77.5638	222	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009739515.1	s__Sphingomonas_G sp009739515	77.5139	271	754	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:52,166] [INFO] GTDB search result was written to GCF_026157035.1_ASM2615703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:52,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:52,170] [INFO] DFAST_QC result json was written to GCF_026157035.1_ASM2615703v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:52,171] [INFO] DFAST_QC completed!
[2024-01-24 15:27:52,171] [INFO] Total running time: 0h1m1s