[2024-01-24 11:22:49,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,436] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,436] [INFO] DQC Reference Directory: /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference
[2024-01-24 11:22:50,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,643] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,644] [INFO] Running command: gunzip -c /var/lib/cwl/stgd4ac1c56-efd5-42f8-8199-685387cad006/GCF_014638565.1_ASM1463856v1_genomic.fna.gz | prodigal -d GCF_014638565.1_ASM1463856v1_genomic.fna/cds.fna -a GCF_014638565.1_ASM1463856v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:04,247] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:04,248] [INFO] Task started: HMMsearch
[2024-01-24 11:23:04,248] [INFO] Running command: hmmsearch --tblout GCF_014638565.1_ASM1463856v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/reference_markers.hmm GCF_014638565.1_ASM1463856v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:04,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:04,522] [INFO] Found 6/6 markers.
[2024-01-24 11:23:04,559] [INFO] Query marker FASTA was written to GCF_014638565.1_ASM1463856v1_genomic.fna/markers.fasta
[2024-01-24 11:23:04,560] [INFO] Task started: Blastn
[2024-01-24 11:23:04,560] [INFO] Running command: blastn -query GCF_014638565.1_ASM1463856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/reference_markers.fasta -out GCF_014638565.1_ASM1463856v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:05,509] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:05,513] [INFO] Selected 17 target genomes.
[2024-01-24 11:23:05,513] [INFO] Target genome list was writen to GCF_014638565.1_ASM1463856v1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:05,521] [INFO] Task started: fastANI
[2024-01-24 11:23:05,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ac1c56-efd5-42f8-8199-685387cad006/GCF_014638565.1_ASM1463856v1_genomic.fna.gz --refList GCF_014638565.1_ASM1463856v1_genomic.fna/target_genomes.txt --output GCF_014638565.1_ASM1463856v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:21,251] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:21,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:21,253] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:21,280] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:23:21,280] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:21,281] [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
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	100.0	1474	1474	95	conclusive
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	99.999	1474	1474	95	conclusive
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	79.4471	612	1474	95	below_threshold
Devosia elaeis	strain=S37	GCA_001650025.1	1770058	1770058	type	True	79.1724	518	1474	95	below_threshold
Devosia ginsengisoli	strain=Gsoil 520	GCA_007859655.1	400770	400770	type	True	79.1433	589	1474	95	below_threshold
Devosia salina	strain=SCS-3	GCA_019504385.1	2860336	2860336	type	True	79.133	532	1474	95	below_threshold
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	79.1017	613	1474	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	79.0577	511	1474	95	below_threshold
Devosia sediminis	strain=MSA67	GCA_016411825.1	2798801	2798801	type	True	78.8937	509	1474	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	78.8621	561	1474	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.795	539	1474	95	below_threshold
Devosia indica	strain=IO390501	GCA_003056405.1	2079253	2079253	type	True	78.5331	446	1474	95	below_threshold
Devosia psychrophila	strain=CGMCC 1.10210	GCA_900112505.1	728005	728005	type	True	78.2305	466	1474	95	below_threshold
Devosia psychrophila	strain=Cr7-05	GCA_000971275.1	728005	728005	type	True	78.1821	470	1474	95	below_threshold
Shinella zoogloeoides	strain=ATCC 19623	GCA_020883495.1	352475	352475	type	True	77.2869	254	1474	95	below_threshold
Xanthobacter dioxanivorans	strain=YN2	GCA_016807805.1	2528964	2528964	type	True	76.746	220	1474	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.2461	274	1474	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:21,283] [INFO] DFAST Taxonomy check result was written to GCF_014638565.1_ASM1463856v1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:21,283] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:21,283] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:21,284] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/checkm_data
[2024-01-24 11:23:21,285] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:21,330] [INFO] Task started: CheckM
[2024-01-24 11:23:21,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014638565.1_ASM1463856v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014638565.1_ASM1463856v1_genomic.fna/checkm_input GCF_014638565.1_ASM1463856v1_genomic.fna/checkm_result
[2024-01-24 11:24:02,651] [INFO] Task succeeded: CheckM
[2024-01-24 11:24:02,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:24:02,675] [INFO] ===== Completeness check finished =====
[2024-01-24 11:24:02,676] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:24:02,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014638565.1_ASM1463856v1_genomic.fna/markers.fasta)
[2024-01-24 11:24:02,677] [INFO] Task started: Blastn
[2024-01-24 11:24:02,677] [INFO] Running command: blastn -query GCF_014638565.1_ASM1463856v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfe666b7b-af81-4219-bd30-96db3968f6f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_014638565.1_ASM1463856v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:24:04,631] [INFO] Task succeeded: Blastn
[2024-01-24 11:24:04,635] [INFO] Selected 15 target genomes.
[2024-01-24 11:24:04,635] [INFO] Target genome list was writen to GCF_014638565.1_ASM1463856v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:24:04,668] [INFO] Task started: fastANI
[2024-01-24 11:24:04,669] [INFO] Running command: fastANI --query /var/lib/cwl/stgd4ac1c56-efd5-42f8-8199-685387cad006/GCF_014638565.1_ASM1463856v1_genomic.fna.gz --refList GCF_014638565.1_ASM1463856v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014638565.1_ASM1463856v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:19,325] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:19,345] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:19,345] [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_008000755.1	s__Youhaiella tibetensis	99.999	1474	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Youhaiella	95.0	99.26	98.52	0.98	0.97	3	conclusive
GCF_016801025.1	s__Paradevosia shaoguanensis	85.2575	1058	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Paradevosia	95.0	97.16	97.13	0.92	0.92	4	-
GCA_017307495.1	s__Devosia_A sp017307495	79.5183	555	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_000969415.1	s__Devosia geojensis	79.4575	611	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	79.2614	647	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCF_001426345.1	s__Devosia sp001426345	79.2023	578	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873135.1	s__Devosia_A sp014873135	79.1817	573	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650025.1	s__Devosia elaeis	79.1762	518	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	79.1588	584	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_005222805.1	s__Devosia sp005222805	79.1569	531	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425235.1	s__Devosia_A sp001425235	79.1176	635	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCF_000970465.2	s__Devosia_A insulae	79.0974	614	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402915.1	s__Devosia_A sp001402915	79.0788	626	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014860165.1	s__Devosia sp014860165	79.0652	548	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	78.9298	582	1474	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:19,347] [INFO] GTDB search result was written to GCF_014638565.1_ASM1463856v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:19,348] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:19,351] [INFO] DFAST_QC result json was written to GCF_014638565.1_ASM1463856v1_genomic.fna/dqc_result.json
[2024-01-24 11:24:19,352] [INFO] DFAST_QC completed!
[2024-01-24 11:24:19,352] [INFO] Total running time: 0h1m30s