[2023-03-16 10:08:11,070] [INFO] DFAST_QC pipeline started.
[2023-03-16 10:08:11,070] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 10:08:11,070] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference
[2023-03-16 10:08:12,212] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 10:08:12,212] [INFO] Task started: Prodigal
[2023-03-16 10:08:12,212] [INFO] Running command: cat /var/lib/cwl/stg372de6d2-4483-402a-8ab7-4aae5a56cf11/OceanDNA-b32282.fa | prodigal -d OceanDNA-b32282/cds.fna -a OceanDNA-b32282/protein.faa -g 11 -q > /dev/null
[2023-03-16 10:08:32,427] [INFO] Task succeeded: Prodigal
[2023-03-16 10:08:32,427] [INFO] Task started: HMMsearch
[2023-03-16 10:08:32,427] [INFO] Running command: hmmsearch --tblout OceanDNA-b32282/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/reference_markers.hmm OceanDNA-b32282/protein.faa > /dev/null
[2023-03-16 10:08:32,636] [INFO] Task succeeded: HMMsearch
[2023-03-16 10:08:32,637] [INFO] Found 6/6 markers.
[2023-03-16 10:08:32,657] [INFO] Query marker FASTA was written to OceanDNA-b32282/markers.fasta
[2023-03-16 10:08:32,658] [INFO] Task started: Blastn
[2023-03-16 10:08:32,658] [INFO] Running command: blastn -query OceanDNA-b32282/markers.fasta -db /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/reference_markers.fasta -out OceanDNA-b32282/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:08:33,372] [INFO] Task succeeded: Blastn
[2023-03-16 10:08:33,373] [INFO] Selected 16 target genomes.
[2023-03-16 10:08:33,373] [INFO] Target genome list was writen to OceanDNA-b32282/target_genomes.txt
[2023-03-16 10:08:33,395] [INFO] Task started: fastANI
[2023-03-16 10:08:33,396] [INFO] Running command: fastANI --query /var/lib/cwl/stg372de6d2-4483-402a-8ab7-4aae5a56cf11/OceanDNA-b32282.fa --refList OceanDNA-b32282/target_genomes.txt --output OceanDNA-b32282/fastani_result.tsv --threads 1
[2023-03-16 10:08:42,669] [INFO] Task succeeded: fastANI
[2023-03-16 10:08:42,670] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 10:08:42,670] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 10:08:42,679] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 10:08:42,680] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 10:08:42,680] [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	83.2013	712	1076	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.2456	300	1076	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.0269	342	1076	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.948	336	1076	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.6828	341	1076	95	below_threshold
Sphingomonas lacunae	strain=CSW-10	GCA_012979535.1	2698828	2698828	type	True	76.7025	104	1076	95	below_threshold
Blastomonas fulva	strain=T2	GCA_003431825.1	1550728	1550728	type	True	76.5213	168	1076	95	below_threshold
Blastomonas aquatica	strain=CGMCC 1.12851	GCA_014639875.1	1510276	1510276	type	True	76.5128	146	1076	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	76.4509	121	1076	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.4386	136	1076	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	76.3077	145	1076	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	76.233	115	1076	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	76.155	117	1076	95	below_threshold
Tsuneonella flava	strain=MS1-4	GCA_002870965.1	2055955	2055955	type	True	75.9868	79	1076	95	below_threshold
Tsuneonella suprasediminis	strain=Ery12	GCA_003605755.1	2306996	2306996	type	True	75.8603	99	1076	95	below_threshold
Qipengyuania aestuarii	strain=GH1	GCA_019711535.1	2867241	2867241	type	True	75.7957	92	1076	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 10:08:42,680] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32282/tc_result.tsv
[2023-03-16 10:08:42,680] [INFO] ===== Taxonomy check completed =====
[2023-03-16 10:08:42,680] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 10:08:42,680] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/checkm_data
[2023-03-16 10:08:42,681] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 10:08:42,685] [INFO] Task started: CheckM
[2023-03-16 10:08:42,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32282/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32282/checkm_input OceanDNA-b32282/checkm_result
[2023-03-16 10:09:33,697] [INFO] Task succeeded: CheckM
[2023-03-16 10:09:33,697] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.89%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 10:09:33,700] [INFO] ===== Completeness check finished =====
[2023-03-16 10:09:33,700] [INFO] ===== Start GTDB Search =====
[2023-03-16 10:09:33,700] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32282/markers.fasta)
[2023-03-16 10:09:33,701] [INFO] Task started: Blastn
[2023-03-16 10:09:33,701] [INFO] Running command: blastn -query OceanDNA-b32282/markers.fasta -db /var/lib/cwl/stgb5165f6c-bbeb-4d93-a9d6-3a5f97ae9694/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32282/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 10:09:34,994] [INFO] Task succeeded: Blastn
[2023-03-16 10:09:34,995] [INFO] Selected 11 target genomes.
[2023-03-16 10:09:34,995] [INFO] Target genome list was writen to OceanDNA-b32282/target_genomes_gtdb.txt
[2023-03-16 10:09:35,032] [INFO] Task started: fastANI
[2023-03-16 10:09:35,032] [INFO] Running command: fastANI --query /var/lib/cwl/stg372de6d2-4483-402a-8ab7-4aae5a56cf11/OceanDNA-b32282.fa --refList OceanDNA-b32282/target_genomes_gtdb.txt --output OceanDNA-b32282/fastani_result_gtdb.tsv --threads 1
[2023-03-16 10:09:42,986] [INFO] Task succeeded: fastANI
[2023-03-16 10:09:42,993] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 10:09:42,993] [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_001586275.1	s__Parasphingorhabdus sp001586275	85.9281	814	1076	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	84.2055	759	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	83.6531	480	1076	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	83.4171	588	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204445.1	s__Parasphingorhabdus sp013204445	83.3297	456	1076	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	83.2913	583	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	83.2137	711	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002218195.1	s__Parasphingorhabdus sp002218195	82.8855	721	1076	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	82.8467	716	1076	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	82.5266	711	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	81.8297	656	1076	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 10:09:42,993] [INFO] GTDB search result was written to OceanDNA-b32282/result_gtdb.tsv
[2023-03-16 10:09:42,993] [INFO] ===== GTDB Search completed =====
[2023-03-16 10:09:42,995] [INFO] DFAST_QC result json was written to OceanDNA-b32282/dqc_result.json
[2023-03-16 10:09:42,995] [INFO] DFAST_QC completed!
[2023-03-16 10:09:42,995] [INFO] Total running time: 0h1m32s