[2023-03-19 03:38:32,435] [INFO] DFAST_QC pipeline started.
[2023-03-19 03:38:32,435] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 03:38:32,435] [INFO] DQC Reference Directory: /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference
[2023-03-19 03:38:33,562] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 03:38:33,562] [INFO] Task started: Prodigal
[2023-03-19 03:38:33,562] [INFO] Running command: cat /var/lib/cwl/stgf149278b-9653-409d-b07d-c6488c3a0b01/OceanDNA-b32055.fa | prodigal -d OceanDNA-b32055/cds.fna -a OceanDNA-b32055/protein.faa -g 11 -q > /dev/null
[2023-03-19 03:38:43,660] [INFO] Task succeeded: Prodigal
[2023-03-19 03:38:43,660] [INFO] Task started: HMMsearch
[2023-03-19 03:38:43,660] [INFO] Running command: hmmsearch --tblout OceanDNA-b32055/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/reference_markers.hmm OceanDNA-b32055/protein.faa > /dev/null
[2023-03-19 03:38:43,816] [INFO] Task succeeded: HMMsearch
[2023-03-19 03:38:43,817] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf149278b-9653-409d-b07d-c6488c3a0b01/OceanDNA-b32055.fa]
[2023-03-19 03:38:43,834] [INFO] Query marker FASTA was written to OceanDNA-b32055/markers.fasta
[2023-03-19 03:38:43,834] [INFO] Task started: Blastn
[2023-03-19 03:38:43,834] [INFO] Running command: blastn -query OceanDNA-b32055/markers.fasta -db /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/reference_markers.fasta -out OceanDNA-b32055/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:38:44,404] [INFO] Task succeeded: Blastn
[2023-03-19 03:38:44,405] [INFO] Selected 12 target genomes.
[2023-03-19 03:38:44,405] [INFO] Target genome list was writen to OceanDNA-b32055/target_genomes.txt
[2023-03-19 03:38:44,412] [INFO] Task started: fastANI
[2023-03-19 03:38:44,412] [INFO] Running command: fastANI --query /var/lib/cwl/stgf149278b-9653-409d-b07d-c6488c3a0b01/OceanDNA-b32055.fa --refList OceanDNA-b32055/target_genomes.txt --output OceanDNA-b32055/fastani_result.tsv --threads 1
[2023-03-19 03:38:51,924] [INFO] Task succeeded: fastANI
[2023-03-19 03:38:51,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 03:38:51,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 03:38:51,932] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 03:38:51,932] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-19 03:38:51,932] [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
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	80.082	222	460	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	78.0156	120	460	95	below_threshold
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	77.9492	124	460	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	77.5399	105	460	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.5327	110	460	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.4373	84	460	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	77.2408	108	460	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	77.2168	109	460	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	77.1707	101	460	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	76.9712	75	460	95	below_threshold
Sphingomonas colocasiae	strain=JCM 31229	GCA_019880585.1	1848973	1848973	type	True	76.895	129	460	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	76.8407	99	460	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-19 03:38:51,933] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32055/tc_result.tsv
[2023-03-19 03:38:51,933] [INFO] ===== Taxonomy check completed =====
[2023-03-19 03:38:51,933] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 03:38:51,933] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/checkm_data
[2023-03-19 03:38:51,933] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 03:38:51,937] [INFO] Task started: CheckM
[2023-03-19 03:38:51,937] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32055/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32055/checkm_input OceanDNA-b32055/checkm_result
[2023-03-19 03:39:21,310] [INFO] Task succeeded: CheckM
[2023-03-19 03:39:21,310] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 03:39:21,312] [INFO] ===== Completeness check finished =====
[2023-03-19 03:39:21,312] [INFO] ===== Start GTDB Search =====
[2023-03-19 03:39:21,313] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32055/markers.fasta)
[2023-03-19 03:39:21,313] [INFO] Task started: Blastn
[2023-03-19 03:39:21,313] [INFO] Running command: blastn -query OceanDNA-b32055/markers.fasta -db /var/lib/cwl/stgd5f40764-7f8d-472f-8e33-a6ec22ca84a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32055/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 03:39:22,161] [INFO] Task succeeded: Blastn
[2023-03-19 03:39:22,162] [INFO] Selected 7 target genomes.
[2023-03-19 03:39:22,162] [INFO] Target genome list was writen to OceanDNA-b32055/target_genomes_gtdb.txt
[2023-03-19 03:39:22,170] [INFO] Task started: fastANI
[2023-03-19 03:39:22,170] [INFO] Running command: fastANI --query /var/lib/cwl/stgf149278b-9653-409d-b07d-c6488c3a0b01/OceanDNA-b32055.fa --refList OceanDNA-b32055/target_genomes_gtdb.txt --output OceanDNA-b32055/fastani_result_gtdb.tsv --threads 1
[2023-03-19 03:39:26,512] [INFO] Task succeeded: fastANI
[2023-03-19 03:39:26,517] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 03:39:26,517] [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
GCA_018823325.1	s__Sphingobium sp018823325	96.3515	395	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	0.97	0.94	4	conclusive
GCF_014201265.1	s__Sphingobium sp014201265	83.725	331	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000283515.1	s__Sphingobium sp000283515	79.9796	240	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.32	96.27	0.90	0.89	5	-
GCA_017304105.1	s__Sphingobium sp017304105	79.8909	207	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	79.7263	223	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899715.1	s__Sphingobium sp001899715	79.2775	215	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017744605.1	s__Sphingobium sp017744605	78.7094	156	460	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 03:39:26,517] [INFO] GTDB search result was written to OceanDNA-b32055/result_gtdb.tsv
[2023-03-19 03:39:26,517] [INFO] ===== GTDB Search completed =====
[2023-03-19 03:39:26,518] [INFO] DFAST_QC result json was written to OceanDNA-b32055/dqc_result.json
[2023-03-19 03:39:26,519] [INFO] DFAST_QC completed!
[2023-03-19 03:39:26,519] [INFO] Total running time: 0h0m54s