[2024-01-24 10:57:38,950] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,952] [INFO] DQC Reference Directory: /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference
[2024-01-24 10:57:40,320] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,321] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,321] [INFO] Running command: gunzip -c /var/lib/cwl/stg44f5cef7-6ea0-41fb-988d-e82108553c22/GCF_019930585.1_ASM1993058v1_genomic.fna.gz | prodigal -d GCF_019930585.1_ASM1993058v1_genomic.fna/cds.fna -a GCF_019930585.1_ASM1993058v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:52,903] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:52,903] [INFO] Task started: HMMsearch
[2024-01-24 10:57:52,903] [INFO] Running command: hmmsearch --tblout GCF_019930585.1_ASM1993058v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/reference_markers.hmm GCF_019930585.1_ASM1993058v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:53,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:53,203] [INFO] Found 6/6 markers.
[2024-01-24 10:57:53,244] [INFO] Query marker FASTA was written to GCF_019930585.1_ASM1993058v1_genomic.fna/markers.fasta
[2024-01-24 10:57:53,245] [INFO] Task started: Blastn
[2024-01-24 10:57:53,245] [INFO] Running command: blastn -query GCF_019930585.1_ASM1993058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/reference_markers.fasta -out GCF_019930585.1_ASM1993058v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:54,374] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:54,378] [INFO] Selected 21 target genomes.
[2024-01-24 10:57:54,378] [INFO] Target genome list was writen to GCF_019930585.1_ASM1993058v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:54,388] [INFO] Task started: fastANI
[2024-01-24 10:57:54,388] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f5cef7-6ea0-41fb-988d-e82108553c22/GCF_019930585.1_ASM1993058v1_genomic.fna.gz --refList GCF_019930585.1_ASM1993058v1_genomic.fna/target_genomes.txt --output GCF_019930585.1_ASM1993058v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:12,055] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:12,056] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:12,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:12,077] [INFO] Found 21 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:58:12,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:58:12,077] [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	80.1474	515	1432	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	79.9242	516	1432	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	79.6448	526	1432	95	below_threshold
Sphingomonas oleivorans	strain=FW-11	GCA_003050615.1	1735121	1735121	type	True	79.5186	467	1432	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	79.4549	449	1432	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	79.431	531	1432	95	below_threshold
Sphingomonas jatrophae	strain=S5-249	GCA_900113315.1	1166337	1166337	type	True	79.3967	517	1432	95	below_threshold
Rhizorhabdus histidinilytica	strain=UM2	GCA_900167915.1	439228	439228	type	True	79.3766	505	1432	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	79.1285	565	1432	95	below_threshold
Sphingomonas fennica	strain=K101	GCA_003034225.1	114404	114404	type	True	79.1158	510	1432	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	79.0641	430	1432	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.9674	475	1432	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.9582	492	1432	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	78.8973	484	1432	95	below_threshold
Sphingomonas laterariae	strain=LNB2	GCA_900188165.1	861865	861865	type	True	78.8238	441	1432	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.7936	516	1432	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.7755	399	1432	95	below_threshold
Sphingomonas horti	strain=MAH-20	GCA_009753715.1	2682842	2682842	type	True	78.7007	395	1432	95	below_threshold
Sphingomonas parva	strain=17J27-24	GCA_004564275.1	2555898	2555898	type	True	78.6331	404	1432	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	78.1144	414	1432	95	below_threshold
Sphingobium phenoxybenzoativorans	strain=SC_3	GCA_001757355.1	1592790	1592790	type	True	77.9286	309	1432	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:12,079] [INFO] DFAST Taxonomy check result was written to GCF_019930585.1_ASM1993058v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:12,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:12,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:12,081] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/checkm_data
[2024-01-24 10:58:12,082] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:12,127] [INFO] Task started: CheckM
[2024-01-24 10:58:12,128] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019930585.1_ASM1993058v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019930585.1_ASM1993058v1_genomic.fna/checkm_input GCF_019930585.1_ASM1993058v1_genomic.fna/checkm_result
[2024-01-24 10:58:51,414] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:51,415] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:51,436] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:51,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:51,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019930585.1_ASM1993058v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:51,437] [INFO] Task started: Blastn
[2024-01-24 10:58:51,438] [INFO] Running command: blastn -query GCF_019930585.1_ASM1993058v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6134579e-d1ea-4e26-8a7d-5ff11ebdcfc8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019930585.1_ASM1993058v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:53,685] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:53,689] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:53,689] [INFO] Target genome list was writen to GCF_019930585.1_ASM1993058v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:53,735] [INFO] Task started: fastANI
[2024-01-24 10:58:53,735] [INFO] Running command: fastANI --query /var/lib/cwl/stg44f5cef7-6ea0-41fb-988d-e82108553c22/GCF_019930585.1_ASM1993058v1_genomic.fna.gz --refList GCF_019930585.1_ASM1993058v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019930585.1_ASM1993058v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:08,851] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:08,874] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:59:08,874] [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_903644055.1	s__Sphingomonas_I sp903644055	80.6997	385	1432	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	80.4596	631	1432	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_003391115.1	s__Sphingomonas_I crusticola	80.1367	516	1432	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_013778325.1	s__Sphingomonas_N chungangi	79.6447	526	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003248515.1	s__Sphingomonas_I sp003248515	79.593	557	1432	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	79.5696	544	1432	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_003050615.1	s__Sphingomonas_H oleivorans	79.5511	464	1432	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_019239915.1	s__Sphingomonas_N sp019239915	79.4001	444	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113315.1	s__Sphingomonas_G jatrophae	79.3677	517	1432	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_001429065.1	s__Rhizorhabdus sp001429065	79.3389	461	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Rhizorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034225.1	s__Sphingomonas_E fennica	79.1278	510	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_E	95.0	98.08	97.94	0.82	0.81	3	-
GCF_014641735.1	s__Sphingomonas metalli	78.8924	478	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188165.1	s__Sphingomonas_E laterariae	78.8387	439	1432	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_009753715.1	s__Sphingomonas_B horti	78.6727	399	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002127225.1	s__Sphingomonas sp002127225	78.6643	458	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320075.1	s__Allosphingosinicella sp011320075	78.6055	346	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129465.1	s__Allosphingosinicella humi	78.5415	316	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Allosphingosinicella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001757355.1	s__Sphingobium phenoxybenzoativorans	77.9365	309	1432	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.17	96.17	0.74	0.74	2	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:08,876] [INFO] GTDB search result was written to GCF_019930585.1_ASM1993058v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:08,877] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:08,881] [INFO] DFAST_QC result json was written to GCF_019930585.1_ASM1993058v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:08,881] [INFO] DFAST_QC completed!
[2024-01-24 10:59:08,881] [INFO] Total running time: 0h1m30s