[2023-03-15 11:22:20,469] [INFO] DFAST_QC pipeline started.
[2023-03-15 11:22:20,469] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 11:22:20,470] [INFO] DQC Reference Directory: /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference
[2023-03-15 11:22:21,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 11:22:21,949] [INFO] Task started: Prodigal
[2023-03-15 11:22:21,949] [INFO] Running command: cat /var/lib/cwl/stgc2397b87-16bb-4985-84cb-9028adf00527/OceanDNA-b32138.fa | prodigal -d OceanDNA-b32138/cds.fna -a OceanDNA-b32138/protein.faa -g 11 -q > /dev/null
[2023-03-15 11:22:36,467] [INFO] Task succeeded: Prodigal
[2023-03-15 11:22:36,467] [INFO] Task started: HMMsearch
[2023-03-15 11:22:36,467] [INFO] Running command: hmmsearch --tblout OceanDNA-b32138/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/reference_markers.hmm OceanDNA-b32138/protein.faa > /dev/null
[2023-03-15 11:22:36,662] [INFO] Task succeeded: HMMsearch
[2023-03-15 11:22:36,662] [INFO] Found 6/6 markers.
[2023-03-15 11:22:36,678] [INFO] Query marker FASTA was written to OceanDNA-b32138/markers.fasta
[2023-03-15 11:22:36,679] [INFO] Task started: Blastn
[2023-03-15 11:22:36,679] [INFO] Running command: blastn -query OceanDNA-b32138/markers.fasta -db /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/reference_markers.fasta -out OceanDNA-b32138/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:22:37,541] [INFO] Task succeeded: Blastn
[2023-03-15 11:22:37,541] [INFO] Selected 13 target genomes.
[2023-03-15 11:22:37,542] [INFO] Target genome list was writen to OceanDNA-b32138/target_genomes.txt
[2023-03-15 11:22:37,549] [INFO] Task started: fastANI
[2023-03-15 11:22:37,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2397b87-16bb-4985-84cb-9028adf00527/OceanDNA-b32138.fa --refList OceanDNA-b32138/target_genomes.txt --output OceanDNA-b32138/fastani_result.tsv --threads 1
[2023-03-15 11:22:47,770] [INFO] Task succeeded: fastANI
[2023-03-15 11:22:47,771] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 11:22:47,771] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 11:22:47,780] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 11:22:47,780] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 11:22:47,780] [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 echinoides	strain=ATCC 14820	GCA_000241465.1	59803	59803	type	True	91.5477	681	769	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	82.8502	551	769	95	below_threshold
Sphingomonas psychrolutea	strain=CGMCC 1.10106	GCA_014636175.1	1259676	1259676	type	True	82.6287	502	769	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.7218	410	769	95	below_threshold
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	80.6499	417	769	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	80.5331	413	769	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	80.2081	417	769	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.0452	308	769	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	78.894	327	769	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	78.8382	381	769	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.7809	341	769	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	78.7757	333	769	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	78.77	269	769	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 11:22:47,780] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32138/tc_result.tsv
[2023-03-15 11:22:47,781] [INFO] ===== Taxonomy check completed =====
[2023-03-15 11:22:47,781] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 11:22:47,781] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/checkm_data
[2023-03-15 11:22:47,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 11:22:47,995] [INFO] Task started: CheckM
[2023-03-15 11:22:47,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32138/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32138/checkm_input OceanDNA-b32138/checkm_result
[2023-03-15 11:23:26,543] [INFO] Task succeeded: CheckM
[2023-03-15 11:23:26,544] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 11:23:26,546] [INFO] ===== Completeness check finished =====
[2023-03-15 11:23:26,546] [INFO] ===== Start GTDB Search =====
[2023-03-15 11:23:26,546] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32138/markers.fasta)
[2023-03-15 11:23:26,548] [INFO] Task started: Blastn
[2023-03-15 11:23:26,548] [INFO] Running command: blastn -query OceanDNA-b32138/markers.fasta -db /var/lib/cwl/stge056a893-a700-46ad-b4d7-533615d04c57/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32138/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 11:23:28,210] [INFO] Task succeeded: Blastn
[2023-03-15 11:23:28,211] [INFO] Selected 10 target genomes.
[2023-03-15 11:23:28,211] [INFO] Target genome list was writen to OceanDNA-b32138/target_genomes_gtdb.txt
[2023-03-15 11:23:28,216] [INFO] Task started: fastANI
[2023-03-15 11:23:28,216] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2397b87-16bb-4985-84cb-9028adf00527/OceanDNA-b32138.fa --refList OceanDNA-b32138/target_genomes_gtdb.txt --output OceanDNA-b32138/fastani_result_gtdb.tsv --threads 1
[2023-03-15 11:23:36,661] [INFO] Task succeeded: fastANI
[2023-03-15 11:23:36,667] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 11:23:36,667] [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_000797515.1	s__Sphingomonas sp000797515	98.7036	673	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.00	97.12	0.86	0.75	5	conclusive
GCF_000241465.1	s__Sphingomonas echinoides	91.5477	681	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.65	96.65	0.85	0.85	2	-
GCF_006439055.1	s__Sphingomonas glacialis_A	83.0733	541	769	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	82.8434	544	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	82.837	553	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_014636175.1	s__Sphingomonas psychrolutea	82.6339	502	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013374095.1	s__Sphingomonas sp013374095	82.5879	509	769	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	81.8318	491	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.28	96.28	0.82	0.82	2	-
GCF_004208535.1	s__Sphingomonas populi	80.6813	414	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423845.1	s__Sphingomonas sp001423845	80.5856	433	769	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 11:23:36,668] [INFO] GTDB search result was written to OceanDNA-b32138/result_gtdb.tsv
[2023-03-15 11:23:36,668] [INFO] ===== GTDB Search completed =====
[2023-03-15 11:23:36,669] [INFO] DFAST_QC result json was written to OceanDNA-b32138/dqc_result.json
[2023-03-15 11:23:36,669] [INFO] DFAST_QC completed!
[2023-03-15 11:23:36,670] [INFO] Total running time: 0h1m16s