[2024-01-24 11:34:52,839] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:52,843] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:52,843] [INFO] DQC Reference Directory: /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference
[2024-01-24 11:34:55,645] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:55,646] [INFO] Task started: Prodigal
[2024-01-24 11:34:55,647] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0b7f802-5812-41fa-974a-effe50a7bc1c/GCF_014653575.1_ASM1465357v1_genomic.fna.gz | prodigal -d GCF_014653575.1_ASM1465357v1_genomic.fna/cds.fna -a GCF_014653575.1_ASM1465357v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:08,706] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:08,707] [INFO] Task started: HMMsearch
[2024-01-24 11:35:08,707] [INFO] Running command: hmmsearch --tblout GCF_014653575.1_ASM1465357v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/reference_markers.hmm GCF_014653575.1_ASM1465357v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:08,997] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:08,999] [INFO] Found 6/6 markers.
[2024-01-24 11:35:09,042] [INFO] Query marker FASTA was written to GCF_014653575.1_ASM1465357v1_genomic.fna/markers.fasta
[2024-01-24 11:35:09,042] [INFO] Task started: Blastn
[2024-01-24 11:35:09,042] [INFO] Running command: blastn -query GCF_014653575.1_ASM1465357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/reference_markers.fasta -out GCF_014653575.1_ASM1465357v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:10,045] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:10,049] [INFO] Selected 16 target genomes.
[2024-01-24 11:35:10,050] [INFO] Target genome list was writen to GCF_014653575.1_ASM1465357v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:10,057] [INFO] Task started: fastANI
[2024-01-24 11:35:10,057] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0b7f802-5812-41fa-974a-effe50a7bc1c/GCF_014653575.1_ASM1465357v1_genomic.fna.gz --refList GCF_014653575.1_ASM1465357v1_genomic.fna/target_genomes.txt --output GCF_014653575.1_ASM1465357v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:25,362] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:25,363] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:25,363] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:25,378] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:25,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:25,378] [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 glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	100.0	1469	1469	95	conclusive
Sphingomonas echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	83.1327	816	1469	95	below_threshold
Sphingomonas psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	82.8876	796	1469	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	81.5021	710	1469	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	81.1909	696	1469	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	80.9414	705	1469	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	80.1401	651	1469	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	80.1268	647	1469	95	below_threshold
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	79.9324	616	1469	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	79.3241	608	1469	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.2989	620	1469	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.2789	617	1469	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.2147	621	1469	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	79.1614	641	1469	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.0538	475	1469	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.0134	477	1469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:25,380] [INFO] DFAST Taxonomy check result was written to GCF_014653575.1_ASM1465357v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:25,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:25,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:25,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/checkm_data
[2024-01-24 11:35:25,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:25,423] [INFO] Task started: CheckM
[2024-01-24 11:35:25,423] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014653575.1_ASM1465357v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014653575.1_ASM1465357v1_genomic.fna/checkm_input GCF_014653575.1_ASM1465357v1_genomic.fna/checkm_result
[2024-01-24 11:36:05,198] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:05,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:05,219] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:05,220] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:05,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014653575.1_ASM1465357v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:05,220] [INFO] Task started: Blastn
[2024-01-24 11:36:05,221] [INFO] Running command: blastn -query GCF_014653575.1_ASM1465357v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg594b693a-effc-4aea-b098-0c96432a06f6/dqc_reference/reference_markers_gtdb.fasta -out GCF_014653575.1_ASM1465357v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:07,185] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:07,189] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:07,189] [INFO] Target genome list was writen to GCF_014653575.1_ASM1465357v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:07,209] [INFO] Task started: fastANI
[2024-01-24 11:36:07,209] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0b7f802-5812-41fa-974a-effe50a7bc1c/GCF_014653575.1_ASM1465357v1_genomic.fna.gz --refList GCF_014653575.1_ASM1465357v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014653575.1_ASM1465357v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:16,658] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:16,670] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:16,670] [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_014653575.1	s__Sphingomonas glacialis	100.0	1469	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	conclusive
GCF_006439055.1	s__Sphingomonas glacialis_A	90.3143	1064	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	89.0055	998	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000251145.1	s__Sphingomonas sp000251145	83.4413	873	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.28	96.28	0.82	0.82	2	-
GCF_000241465.1	s__Sphingomonas echinoides	83.1119	818	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_013374095.1	s__Sphingomonas sp013374095	82.8757	775	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636175.1	s__Sphingomonas psychrolutea	82.8695	798	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000797515.1	s__Sphingomonas sp000797515	82.8072	743	1469	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,672] [INFO] GTDB search result was written to GCF_014653575.1_ASM1465357v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:16,672] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:16,675] [INFO] DFAST_QC result json was written to GCF_014653575.1_ASM1465357v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:16,676] [INFO] DFAST_QC completed!
[2024-01-24 11:36:16,676] [INFO] Total running time: 0h1m24s