[2024-01-25 17:41:50,655] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:41:50,656] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:41:50,656] [INFO] DQC Reference Directory: /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference
[2024-01-25 17:41:51,793] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:41:51,794] [INFO] Task started: Prodigal
[2024-01-25 17:41:51,794] [INFO] Running command: gunzip -c /var/lib/cwl/stg4c87984e-00e4-4eed-b309-efc38f8a6683/GCF_003391115.1_ASM339111v1_genomic.fna.gz | prodigal -d GCF_003391115.1_ASM339111v1_genomic.fna/cds.fna -a GCF_003391115.1_ASM339111v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:42:00,724] [INFO] Task succeeded: Prodigal
[2024-01-25 17:42:00,725] [INFO] Task started: HMMsearch
[2024-01-25 17:42:00,725] [INFO] Running command: hmmsearch --tblout GCF_003391115.1_ASM339111v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/reference_markers.hmm GCF_003391115.1_ASM339111v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:42:00,933] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:42:00,934] [INFO] Found 6/6 markers.
[2024-01-25 17:42:00,969] [INFO] Query marker FASTA was written to GCF_003391115.1_ASM339111v1_genomic.fna/markers.fasta
[2024-01-25 17:42:00,969] [INFO] Task started: Blastn
[2024-01-25 17:42:00,969] [INFO] Running command: blastn -query GCF_003391115.1_ASM339111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/reference_markers.fasta -out GCF_003391115.1_ASM339111v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:01,877] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:01,880] [INFO] Selected 22 target genomes.
[2024-01-25 17:42:01,881] [INFO] Target genome list was writen to GCF_003391115.1_ASM339111v1_genomic.fna/target_genomes.txt
[2024-01-25 17:42:01,899] [INFO] Task started: fastANI
[2024-01-25 17:42:01,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c87984e-00e4-4eed-b309-efc38f8a6683/GCF_003391115.1_ASM339111v1_genomic.fna.gz --refList GCF_003391115.1_ASM339111v1_genomic.fna/target_genomes.txt --output GCF_003391115.1_ASM339111v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:42:20,460] [INFO] Task succeeded: fastANI
[2024-01-25 17:42:20,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:42:20,461] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:42:20,474] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:42:20,474] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:42:20,474] [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 crusticola	strain=MIMD3	GCA_003391115.1	1697973	1697973	type	True	100.0	1122	1122	95	conclusive
Sphingomonas vulcanisoli	strain=CECT 8804	GCA_011761305.1	1658060	1658060	type	True	79.4705	402	1122	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.0308	363	1122	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	78.7538	373	1122	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	78.6331	376	1122	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.5647	357	1122	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	78.5265	379	1122	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	78.4499	327	1122	95	below_threshold
Sphingomonas sanxanigenens	strain=NX02	GCA_000512205.2	397260	397260	type	True	78.4212	372	1122	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.3595	293	1122	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	78.344	391	1122	95	below_threshold
Sphingomonas formosensis	strain=CC-Nfb-2	GCA_009755815.1	861534	861534	type	True	78.2364	372	1122	95	below_threshold
Sphingomonas prati	strain=W18RD	GCA_009755805.1	1843237	1843237	type	True	78.1648	305	1122	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.1638	306	1122	95	below_threshold
Sphingomonas prati	strain=CGMCC 1.15645	GCA_014643515.1	1843237	1843237	type	True	78.1451	310	1122	95	below_threshold
Sphingomonas prati	strain=DSM 103336	GCA_014199405.1	1843237	1843237	type	True	78.1439	306	1122	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.1296	318	1122	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.1067	343	1122	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	78.071	298	1122	95	below_threshold
Sphingomonas kaistensis	strain=DSM 16846	GCA_011927725.1	298708	298708	type	True	78.0358	219	1122	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	77.9796	322	1122	95	below_threshold
Sphingomonas rhizophila	strain=KACC 19189	GCA_014396585.1	2071607	2071607	type	True	77.9118	203	1122	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:42:20,475] [INFO] DFAST Taxonomy check result was written to GCF_003391115.1_ASM339111v1_genomic.fna/tc_result.tsv
[2024-01-25 17:42:20,476] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:42:20,476] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:42:20,476] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/checkm_data
[2024-01-25 17:42:20,477] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:42:20,514] [INFO] Task started: CheckM
[2024-01-25 17:42:20,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003391115.1_ASM339111v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003391115.1_ASM339111v1_genomic.fna/checkm_input GCF_003391115.1_ASM339111v1_genomic.fna/checkm_result
[2024-01-25 17:42:49,519] [INFO] Task succeeded: CheckM
[2024-01-25 17:42:49,520] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:42:49,540] [INFO] ===== Completeness check finished =====
[2024-01-25 17:42:49,540] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:42:49,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003391115.1_ASM339111v1_genomic.fna/markers.fasta)
[2024-01-25 17:42:49,541] [INFO] Task started: Blastn
[2024-01-25 17:42:49,541] [INFO] Running command: blastn -query GCF_003391115.1_ASM339111v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf08bbda3-8e02-45ca-ac41-db90ce9d5507/dqc_reference/reference_markers_gtdb.fasta -out GCF_003391115.1_ASM339111v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:42:51,349] [INFO] Task succeeded: Blastn
[2024-01-25 17:42:51,351] [INFO] Selected 21 target genomes.
[2024-01-25 17:42:51,352] [INFO] Target genome list was writen to GCF_003391115.1_ASM339111v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:42:51,371] [INFO] Task started: fastANI
[2024-01-25 17:42:51,371] [INFO] Running command: fastANI --query /var/lib/cwl/stg4c87984e-00e4-4eed-b309-efc38f8a6683/GCF_003391115.1_ASM339111v1_genomic.fna.gz --refList GCF_003391115.1_ASM339111v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003391115.1_ASM339111v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:43:07,571] [INFO] Task succeeded: fastANI
[2024-01-25 17:43:07,584] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:43:07,584] [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_003391115.1	s__Sphingomonas_I crusticola	100.0	1122	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011761305.1	s__Sphingomonas_I vulcanisoli	79.4457	404	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903644055.1	s__Sphingomonas_I sp903644055	79.3526	319	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113735.1	s__Sphingomonas_I sp013113735	79.1562	466	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003050615.1	s__Sphingomonas_H oleivorans	79.0069	365	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_H	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248515.1	s__Sphingomonas_I sp003248515	78.8916	415	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_I	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871605.1	s__Sphingomonas_N sp903871605	78.7847	380	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	99.98	99.98	0.98	0.98	2	-
GCF_004005865.1	s__Rhizorhabdus crocodyli	78.718	361	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018863195.1	s__XMGL2 sp018863195	78.7034	360	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__XMGL2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	78.6064	379	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.5593	358	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	78.4302	345	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_000512205.2	s__Sphingomonas_D sanxanigenens	78.3976	375	1122	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_003129465.1	s__Allosphingosinicella humi	78.1601	253	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	78.1571	307	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCA_001724715.1	s__SCN-67-18 sp001724715	78.1487	286	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__SCN-67-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096895.1	s__Sphingomonas sp003096895	78.1373	374	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643515.1	s__Sphingomonas_G prati	78.1339	311	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_G	95.0	100.00	100.00	1.00	1.00	3	-
GCF_004564275.1	s__Allosphingosinicella parva	78.1298	318	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304125.1	s__Sphingomonas sp017304125	78.0909	206	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011927725.1	s__Sphingomicrobium kaistense	78.0516	218	1122	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:43:07,586] [INFO] GTDB search result was written to GCF_003391115.1_ASM339111v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:43:07,586] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:43:07,590] [INFO] DFAST_QC result json was written to GCF_003391115.1_ASM339111v1_genomic.fna/dqc_result.json
[2024-01-25 17:43:07,590] [INFO] DFAST_QC completed!
[2024-01-25 17:43:07,590] [INFO] Total running time: 0h1m17s