[2024-01-24 12:14:33,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference
[2024-01-24 12:14:35,164] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:35,165] [INFO] Task started: Prodigal
[2024-01-24 12:14:35,165] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a33dbb7-0a14-457d-a03f-444e0cdf0ded/GCF_004005865.1_ASM400586v1_genomic.fna.gz | prodigal -d GCF_004005865.1_ASM400586v1_genomic.fna/cds.fna -a GCF_004005865.1_ASM400586v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:49,599] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:49,599] [INFO] Task started: HMMsearch
[2024-01-24 12:14:49,599] [INFO] Running command: hmmsearch --tblout GCF_004005865.1_ASM400586v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/reference_markers.hmm GCF_004005865.1_ASM400586v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:49,893] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:49,894] [INFO] Found 6/6 markers.
[2024-01-24 12:14:49,941] [INFO] Query marker FASTA was written to GCF_004005865.1_ASM400586v1_genomic.fna/markers.fasta
[2024-01-24 12:14:49,941] [INFO] Task started: Blastn
[2024-01-24 12:14:49,942] [INFO] Running command: blastn -query GCF_004005865.1_ASM400586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/reference_markers.fasta -out GCF_004005865.1_ASM400586v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:50,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:50,969] [INFO] Selected 23 target genomes.
[2024-01-24 12:14:50,970] [INFO] Target genome list was writen to GCF_004005865.1_ASM400586v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:50,979] [INFO] Task started: fastANI
[2024-01-24 12:14:50,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a33dbb7-0a14-457d-a03f-444e0cdf0ded/GCF_004005865.1_ASM400586v1_genomic.fna.gz --refList GCF_004005865.1_ASM400586v1_genomic.fna/target_genomes.txt --output GCF_004005865.1_ASM400586v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:12,411] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:12,411] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:12,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:12,429] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:12,429] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:12,429] [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
Rhizorhabdus dicambivorans	strain=Ndbn-20	GCA_002355275.1	1850238	1850238	type	True	81.0689	649	1624	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	80.9639	675	1624	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	80.0262	600	1624	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	79.6289	533	1624	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.537	468	1624	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.5295	533	1624	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	79.294	474	1624	95	below_threshold
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	79.0682	400	1624	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	79.0276	496	1624	95	below_threshold
Sphingomonas crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	78.9782	337	1624	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.9768	553	1624	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	78.9665	447	1624	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	78.912	435	1624	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.8864	545	1624	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.8065	545	1624	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.7869	522	1624	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.7607	406	1624	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.6599	405	1624	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.6186	404	1624	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.3997	375	1624	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.3658	403	1624	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	78.0812	260	1624	95	below_threshold
Novosphingobium naphthalenivorans	strain=NBRC 102051	GCA_001590985.1	273168	273168	type	True	77.8234	319	1624	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:12,432] [INFO] DFAST Taxonomy check result was written to GCF_004005865.1_ASM400586v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:12,432] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:12,432] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:12,432] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/checkm_data
[2024-01-24 12:15:12,433] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:12,483] [INFO] Task started: CheckM
[2024-01-24 12:15:12,483] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004005865.1_ASM400586v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004005865.1_ASM400586v1_genomic.fna/checkm_input GCF_004005865.1_ASM400586v1_genomic.fna/checkm_result
[2024-01-24 12:15:55,826] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:55,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:55,854] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:55,854] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:55,855] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004005865.1_ASM400586v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:55,855] [INFO] Task started: Blastn
[2024-01-24 12:15:55,855] [INFO] Running command: blastn -query GCF_004005865.1_ASM400586v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg16b741ab-f07f-45a1-9d88-7f0aba910ccf/dqc_reference/reference_markers_gtdb.fasta -out GCF_004005865.1_ASM400586v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:57,738] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:57,742] [INFO] Selected 15 target genomes.
[2024-01-24 12:15:57,743] [INFO] Target genome list was writen to GCF_004005865.1_ASM400586v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:57,753] [INFO] Task started: fastANI
[2024-01-24 12:15:57,753] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a33dbb7-0a14-457d-a03f-444e0cdf0ded/GCF_004005865.1_ASM400586v1_genomic.fna.gz --refList GCF_004005865.1_ASM400586v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004005865.1_ASM400586v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:13,946] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:13,973] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:13,974] [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_004005865.1	s__Rhizorhabdus crocodyli	100.0	1623	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008274695.1	s__Rhizorhabdus montanisoli	89.5789	1097	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001429065.1	s__Rhizorhabdus sp001429065	81.2279	624	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000016765.1	s__Rhizorhabdus wittichii	81.1867	704	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.56	98.46	0.83	0.82	5	-
GCF_900167915.1	s__Rhizorhabdus histidinilytica	80.9998	672	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.24	99.18	0.90	0.89	3	-
GCF_002355275.1	s__Rhizorhabdus dicambivorans	80.9997	655	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	99.99	99.99	1.00	0.99	3	-
GCF_001015195.1	s__Rhizorhabdus sp001015195	80.5427	615	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297635.1	s__Rhizorhabdus sp004297635	80.4937	351	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	98.78	98.78	0.98	0.98	2	-
GCF_900101455.1	s__Rhizorhabdus sp900101455	80.0053	555	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744515.1	s__Rhizorhabdus wittichii_A	79.9241	568	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	79.6198	534	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003240855.1	s__Sphingomonas_L sanxanigenens_A	79.2541	409	1624	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_000512205.2	s__Sphingomonas_D sanxanigenens	78.9929	551	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755815.1	s__Sphingomonas_M formosensis	78.8113	544	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_M	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000333335.1	s__Sphingomonas_N sp000333335	78.7016	402	1624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:13,977] [INFO] GTDB search result was written to GCF_004005865.1_ASM400586v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:13,977] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:13,982] [INFO] DFAST_QC result json was written to GCF_004005865.1_ASM400586v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:13,982] [INFO] DFAST_QC completed!
[2024-01-24 12:16:13,983] [INFO] Total running time: 0h1m40s