[2023-03-16 03:47:32,866] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,866] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,866] [INFO] DQC Reference Directory: /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,534] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,534] [INFO] Running command: cat /var/lib/cwl/stg254fac9e-3c5c-43a3-87d6-83011b353a59/OceanDNA-b32184.fa | prodigal -d OceanDNA-b32184/cds.fna -a OceanDNA-b32184/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:52,608] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:52,608] [INFO] Task started: HMMsearch
[2023-03-16 03:47:52,608] [INFO] Running command: hmmsearch --tblout OceanDNA-b32184/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/reference_markers.hmm OceanDNA-b32184/protein.faa > /dev/null
[2023-03-16 03:47:52,910] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:52,910] [INFO] Found 6/6 markers.
[2023-03-16 03:47:52,929] [INFO] Query marker FASTA was written to OceanDNA-b32184/markers.fasta
[2023-03-16 03:47:52,929] [INFO] Task started: Blastn
[2023-03-16 03:47:52,929] [INFO] Running command: blastn -query OceanDNA-b32184/markers.fasta -db /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/reference_markers.fasta -out OceanDNA-b32184/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:53,698] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:53,699] [INFO] Selected 16 target genomes.
[2023-03-16 03:47:53,699] [INFO] Target genome list was writen to OceanDNA-b32184/target_genomes.txt
[2023-03-16 03:47:53,708] [INFO] Task started: fastANI
[2023-03-16 03:47:53,708] [INFO] Running command: fastANI --query /var/lib/cwl/stg254fac9e-3c5c-43a3-87d6-83011b353a59/OceanDNA-b32184.fa --refList OceanDNA-b32184/target_genomes.txt --output OceanDNA-b32184/fastani_result.tsv --threads 1
[2023-03-16 03:48:05,286] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:05,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:05,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:05,297] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2023-03-16 03:48:05,297] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 03:48:05,297] [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
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	99.5254	938	961	95	conclusive
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.6607	373	961	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.254	380	961	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0192	315	961	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.0062	324	961	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	77.3668	204	961	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.2536	166	961	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	76.9865	143	961	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.9133	154	961	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	76.7611	189	961	95	below_threshold
Sphingomonas hankookensis	strain=KCTC 22579	GCA_022664465.1	563996	563996	type	True	76.7383	157	961	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.7095	158	961	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.6049	141	961	95	below_threshold
Sphingomonas solaris	strain=R4DWN	GCA_007785815.1	2529389	2529389	type	True	76.5243	126	961	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	76.4835	170	961	95	below_threshold
Erythrobacter donghaensis	strain=DSM 16220	GCA_002155425.1	267135	267135	suspected-type	True	76.1987	150	961	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:05,297] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32184/tc_result.tsv
[2023-03-16 03:48:05,297] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:05,297] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:05,298] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/checkm_data
[2023-03-16 03:48:05,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:05,303] [INFO] Task started: CheckM
[2023-03-16 03:48:05,303] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32184/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32184/checkm_input OceanDNA-b32184/checkm_result
[2023-03-16 03:48:51,791] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:51,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:51,793] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:51,794] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:51,794] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32184/markers.fasta)
[2023-03-16 03:48:51,794] [INFO] Task started: Blastn
[2023-03-16 03:48:51,794] [INFO] Running command: blastn -query OceanDNA-b32184/markers.fasta -db /var/lib/cwl/stgd31d4630-1f42-47fb-8fbb-d243eee2f4ff/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32184/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:53,221] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:53,221] [INFO] Selected 10 target genomes.
[2023-03-16 03:48:53,221] [INFO] Target genome list was writen to OceanDNA-b32184/target_genomes_gtdb.txt
[2023-03-16 03:48:53,223] [INFO] Task started: fastANI
[2023-03-16 03:48:53,223] [INFO] Running command: fastANI --query /var/lib/cwl/stg254fac9e-3c5c-43a3-87d6-83011b353a59/OceanDNA-b32184.fa --refList OceanDNA-b32184/target_genomes_gtdb.txt --output OceanDNA-b32184/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:00,414] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:00,421] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 03:49:00,421] [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_013371215.1	s__Parasphingorhabdus flavimaris	99.5254	938	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002218195.1	s__Parasphingorhabdus sp002218195	83.9534	715	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002776575.1	s__Parasphingorhabdus sp002776575	83.8753	739	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	83.5086	714	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479715.1	s__Parasphingorhabdus sp905479715	83.3764	569	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	83.2534	696	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002783865.1	s__Parasphingorhabdus sp002783865	82.6271	533	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	82.5957	449	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002354635.1	s__Parasphingorhabdus sp002354635	82.5269	672	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017498565.1	s__Parasphingorhabdus sp017498565	78.0102	323	961	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:00,421] [INFO] GTDB search result was written to OceanDNA-b32184/result_gtdb.tsv
[2023-03-16 03:49:00,422] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:00,423] [INFO] DFAST_QC result json was written to OceanDNA-b32184/dqc_result.json
[2023-03-16 03:49:00,423] [INFO] DFAST_QC completed!
[2023-03-16 03:49:00,423] [INFO] Total running time: 0h1m28s