[2023-03-16 09:50:49,824] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:50:49,826] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:50:49,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference
[2023-03-16 09:50:50,946] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:50:50,947] [INFO] Task started: Prodigal
[2023-03-16 09:50:50,948] [INFO] Running command: cat /var/lib/cwl/stgdcc53bdb-0b99-49fc-a834-a1a1a98688d7/OceanDNA-b32268.fa | prodigal -d OceanDNA-b32268/cds.fna -a OceanDNA-b32268/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:51:02,639] [INFO] Task succeeded: Prodigal
[2023-03-16 09:51:02,639] [INFO] Task started: HMMsearch
[2023-03-16 09:51:02,639] [INFO] Running command: hmmsearch --tblout OceanDNA-b32268/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/reference_markers.hmm OceanDNA-b32268/protein.faa > /dev/null
[2023-03-16 09:51:02,822] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:51:02,823] [INFO] Found 6/6 markers.
[2023-03-16 09:51:02,850] [INFO] Query marker FASTA was written to OceanDNA-b32268/markers.fasta
[2023-03-16 09:51:02,851] [INFO] Task started: Blastn
[2023-03-16 09:51:02,851] [INFO] Running command: blastn -query OceanDNA-b32268/markers.fasta -db /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/reference_markers.fasta -out OceanDNA-b32268/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:03,568] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:03,573] [INFO] Selected 19 target genomes.
[2023-03-16 09:51:03,573] [INFO] Target genome list was writen to OceanDNA-b32268/target_genomes.txt
[2023-03-16 09:51:03,586] [INFO] Task started: fastANI
[2023-03-16 09:51:03,586] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc53bdb-0b99-49fc-a834-a1a1a98688d7/OceanDNA-b32268.fa --refList OceanDNA-b32268/target_genomes.txt --output OceanDNA-b32268/fastani_result.tsv --threads 1
[2023-03-16 09:51:14,699] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:14,699] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:51:14,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:51:14,711] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:51:14,711] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 09:51:14,711] [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	83.4802	528	630	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.2305	239	630	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.2131	285	630	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.0507	231	630	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.003	254	630	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.7623	139	630	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	76.7251	91	630	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.6647	104	630	95	below_threshold
Parasphingopyxis marina	strain=GrpM-11	GCA_014237875.1	2761622	2761622	type	True	76.6129	106	630	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	76.5708	129	630	95	below_threshold
Rhizorhabdus phycosphaerae	strain=MK52	GCA_011044255.1	2711156	2711156	type	True	76.5107	90	630	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	76.4467	106	630	95	below_threshold
Erythrobacter dokdonensis	strain=DSW-74	GCA_001677335.1	328225	328225	type	True	76.3587	68	630	95	below_threshold
Sphingorhabdus soli	strain=D-2Q-5-6	GCA_007995095.1	2601267	2601267	type	True	76.3534	101	630	95	below_threshold
Erythrobacter dokdonensis	strain=DSM 17193	GCA_002155305.1	328225	328225	type	True	76.3064	70	630	95	below_threshold
Croceicoccus pelagius	strain=Ery9	GCA_001661915.1	1703341	1703341	type	True	76.2761	64	630	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.2292	96	630	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	76.0253	74	630	95	below_threshold
Sphingomonas jaspsi	strain=DSM 18422	GCA_000585415.1	392409	392409	type	True	76.0039	72	630	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 09:51:14,715] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32268/tc_result.tsv
[2023-03-16 09:51:14,720] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:51:14,720] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:51:14,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/checkm_data
[2023-03-16 09:51:14,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:51:14,729] [INFO] Task started: CheckM
[2023-03-16 09:51:14,729] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32268/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32268/checkm_input OceanDNA-b32268/checkm_result
[2023-03-16 09:51:47,624] [INFO] Task succeeded: CheckM
[2023-03-16 09:51:47,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.44%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 09:51:47,746] [INFO] ===== Completeness check finished =====
[2023-03-16 09:51:47,746] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:51:47,746] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32268/markers.fasta)
[2023-03-16 09:51:47,747] [INFO] Task started: Blastn
[2023-03-16 09:51:47,747] [INFO] Running command: blastn -query OceanDNA-b32268/markers.fasta -db /var/lib/cwl/stg32337fd7-557a-4400-b96a-a7792576246b/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32268/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:51:49,043] [INFO] Task succeeded: Blastn
[2023-03-16 09:51:49,048] [INFO] Selected 9 target genomes.
[2023-03-16 09:51:49,048] [INFO] Target genome list was writen to OceanDNA-b32268/target_genomes_gtdb.txt
[2023-03-16 09:51:49,115] [INFO] Task started: fastANI
[2023-03-16 09:51:49,116] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc53bdb-0b99-49fc-a834-a1a1a98688d7/OceanDNA-b32268.fa --refList OceanDNA-b32268/target_genomes_gtdb.txt --output OceanDNA-b32268/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:51:54,585] [INFO] Task succeeded: fastANI
[2023-03-16 09:51:54,591] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 09:51:54,592] [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_905479715.1	s__Parasphingorhabdus sp905479715	98.1286	518	630	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_001586275.1	s__Parasphingorhabdus sp001586275	83.6699	525	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	83.4679	529	630	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	83.4609	530	630	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	82.7796	511	630	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	82.6671	529	630	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	82.6038	416	630	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	82.5419	357	630	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	82.2583	507	630	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 09:51:54,595] [INFO] GTDB search result was written to OceanDNA-b32268/result_gtdb.tsv
[2023-03-16 09:51:54,599] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:51:54,604] [INFO] DFAST_QC result json was written to OceanDNA-b32268/dqc_result.json
[2023-03-16 09:51:54,604] [INFO] DFAST_QC completed!
[2023-03-16 09:51:54,604] [INFO] Total running time: 0h1m5s