[2023-03-15 07:52:40,271] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,271] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference
[2023-03-15 07:52:41,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,614] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,614] [INFO] Running command: cat /var/lib/cwl/stg613bdd0b-07b0-4d4e-ba2c-e0ad5f3780b1/OceanDNA-b32231.fa | prodigal -d OceanDNA-b32231/cds.fna -a OceanDNA-b32231/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:52:56,054] [INFO] Task succeeded: Prodigal
[2023-03-15 07:52:56,054] [INFO] Task started: HMMsearch
[2023-03-15 07:52:56,054] [INFO] Running command: hmmsearch --tblout OceanDNA-b32231/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/reference_markers.hmm OceanDNA-b32231/protein.faa > /dev/null
[2023-03-15 07:52:56,286] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:52:56,287] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg613bdd0b-07b0-4d4e-ba2c-e0ad5f3780b1/OceanDNA-b32231.fa]
[2023-03-15 07:52:56,305] [INFO] Query marker FASTA was written to OceanDNA-b32231/markers.fasta
[2023-03-15 07:52:56,305] [INFO] Task started: Blastn
[2023-03-15 07:52:56,305] [INFO] Running command: blastn -query OceanDNA-b32231/markers.fasta -db /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/reference_markers.fasta -out OceanDNA-b32231/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:52:57,010] [INFO] Task succeeded: Blastn
[2023-03-15 07:52:57,010] [INFO] Selected 9 target genomes.
[2023-03-15 07:52:57,011] [INFO] Target genome list was writen to OceanDNA-b32231/target_genomes.txt
[2023-03-15 07:52:57,015] [INFO] Task started: fastANI
[2023-03-15 07:52:57,015] [INFO] Running command: fastANI --query /var/lib/cwl/stg613bdd0b-07b0-4d4e-ba2c-e0ad5f3780b1/OceanDNA-b32231.fa --refList OceanDNA-b32231/target_genomes.txt --output OceanDNA-b32231/fastani_result.tsv --threads 1
[2023-03-15 07:53:03,099] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:03,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:03,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:03,106] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:53:03,106] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:53:03,106] [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	82.3393	593	770	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.461	358	770	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.7513	239	770	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.6752	261	770	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.524	252	770	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	77.2715	191	770	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	77.1198	177	770	95	below_threshold
Novosphingobium kunmingense	strain=CGMCC 1.12274	GCA_002813245.1	1211806	1211806	type	True	77.0945	162	770	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.0528	185	770	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:03,107] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32231/tc_result.tsv
[2023-03-15 07:53:03,107] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:03,107] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:03,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/checkm_data
[2023-03-15 07:53:03,108] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:03,124] [INFO] Task started: CheckM
[2023-03-15 07:53:03,124] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32231/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32231/checkm_input OceanDNA-b32231/checkm_result
[2023-03-15 07:53:41,773] [INFO] Task succeeded: CheckM
[2023-03-15 07:53:41,774] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.82%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:53:41,776] [INFO] ===== Completeness check finished =====
[2023-03-15 07:53:41,776] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:53:41,776] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32231/markers.fasta)
[2023-03-15 07:53:41,777] [INFO] Task started: Blastn
[2023-03-15 07:53:41,777] [INFO] Running command: blastn -query OceanDNA-b32231/markers.fasta -db /var/lib/cwl/stg8031d315-76dc-4660-8543-b83ebfddcc28/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32231/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:43,061] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:43,061] [INFO] Selected 10 target genomes.
[2023-03-15 07:53:43,062] [INFO] Target genome list was writen to OceanDNA-b32231/target_genomes_gtdb.txt
[2023-03-15 07:53:43,091] [INFO] Task started: fastANI
[2023-03-15 07:53:43,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg613bdd0b-07b0-4d4e-ba2c-e0ad5f3780b1/OceanDNA-b32231.fa --refList OceanDNA-b32231/target_genomes_gtdb.txt --output OceanDNA-b32231/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:53:49,990] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:49,997] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 07:53:49,997] [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_002354635.1	s__Parasphingorhabdus sp002354635	85.4853	658	770	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	83.9659	517	770	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	83.8703	413	770	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	83.2408	612	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCA_002733865.1	s__Parasphingorhabdus sp002733865	83.1937	603	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001586275.1	s__Parasphingorhabdus sp001586275	82.8694	602	770	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	82.5101	608	770	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	82.3484	601	770	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	82.333	594	770	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	81.6557	485	770	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:53:49,997] [INFO] GTDB search result was written to OceanDNA-b32231/result_gtdb.tsv
[2023-03-15 07:53:49,997] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:53:49,998] [INFO] DFAST_QC result json was written to OceanDNA-b32231/dqc_result.json
[2023-03-15 07:53:49,999] [INFO] DFAST_QC completed!
[2023-03-15 07:53:49,999] [INFO] Total running time: 0h1m10s