[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/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,535] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,535] [INFO] Running command: cat /var/lib/cwl/stg4fc3c600-8507-4060-be79-c6ed629fe644/OceanDNA-b32237.fa | prodigal -d OceanDNA-b32237/cds.fna -a OceanDNA-b32237/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:47:53,128] [INFO] Task succeeded: Prodigal
[2023-03-16 03:47:53,128] [INFO] Task started: HMMsearch
[2023-03-16 03:47:53,128] [INFO] Running command: hmmsearch --tblout OceanDNA-b32237/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/reference_markers.hmm OceanDNA-b32237/protein.faa > /dev/null
[2023-03-16 03:47:53,387] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:47:53,388] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4fc3c600-8507-4060-be79-c6ed629fe644/OceanDNA-b32237.fa]
[2023-03-16 03:47:53,408] [INFO] Query marker FASTA was written to OceanDNA-b32237/markers.fasta
[2023-03-16 03:47:53,409] [INFO] Task started: Blastn
[2023-03-16 03:47:53,409] [INFO] Running command: blastn -query OceanDNA-b32237/markers.fasta -db /var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/reference_markers.fasta -out OceanDNA-b32237/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:47:54,159] [INFO] Task succeeded: Blastn
[2023-03-16 03:47:54,160] [INFO] Selected 15 target genomes.
[2023-03-16 03:47:54,160] [INFO] Target genome list was writen to OceanDNA-b32237/target_genomes.txt
[2023-03-16 03:47:54,166] [INFO] Task started: fastANI
[2023-03-16 03:47:54,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc3c600-8507-4060-be79-c6ed629fe644/OceanDNA-b32237.fa --refList OceanDNA-b32237/target_genomes.txt --output OceanDNA-b32237/fastani_result.tsv --threads 1
[2023-03-16 03:48:03,894] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:03,895] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:03,895] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:03,903] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:03,903] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:03,904] [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	81.9558	623	989	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.2179	338	989	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	77.4239	289	989	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	77.3529	254	989	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	77.3112	253	989	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.1567	165	989	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.7957	156	989	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	76.7119	156	989	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	76.691	145	989	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	76.613	152	989	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	76.5857	133	989	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	76.518	143	989	95	below_threshold
Mesorhizobium composti	strain=CC-YTH430	GCA_004801285.1	2675109	2675109	type	True	75.1287	62	989	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:03,904] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32237/tc_result.tsv
[2023-03-16 03:48:03,904] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:03,904] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:03,904] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/checkm_data
[2023-03-16 03:48:03,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:03,909] [INFO] Task started: CheckM
[2023-03-16 03:48:03,909] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32237/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32237/checkm_input OceanDNA-b32237/checkm_result
[2023-03-16 03:48:51,144] [INFO] Task succeeded: CheckM
[2023-03-16 03:48:51,145] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:48:51,147] [INFO] ===== Completeness check finished =====
[2023-03-16 03:48:51,147] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:48:51,147] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32237/markers.fasta)
[2023-03-16 03:48:51,148] [INFO] Task started: Blastn
[2023-03-16 03:48:51,148] [INFO] Running command: blastn -query OceanDNA-b32237/markers.fasta -db /var/lib/cwl/stg55f79da1-6125-4bc4-bee7-da67ac0ef8a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32237/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:52,473] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:52,474] [INFO] Selected 11 target genomes.
[2023-03-16 03:48:52,474] [INFO] Target genome list was writen to OceanDNA-b32237/target_genomes_gtdb.txt
[2023-03-16 03:48:52,498] [INFO] Task started: fastANI
[2023-03-16 03:48:52,498] [INFO] Running command: fastANI --query /var/lib/cwl/stg4fc3c600-8507-4060-be79-c6ed629fe644/OceanDNA-b32237.fa --refList OceanDNA-b32237/target_genomes_gtdb.txt --output OceanDNA-b32237/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:00,101] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:00,108] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:49:00,109] [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	85.2154	700	989	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	83.9799	535	989	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	83.5922	444	989	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	82.9807	676	989	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	82.5363	662	989	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	82.3368	627	989	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	82.0782	404	989	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	81.964	622	989	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	81.8774	637	989	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	81.7836	613	989	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	81.705	502	989	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 03:49:00,109] [INFO] GTDB search result was written to OceanDNA-b32237/result_gtdb.tsv
[2023-03-16 03:49:00,109] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:00,110] [INFO] DFAST_QC result json was written to OceanDNA-b32237/dqc_result.json
[2023-03-16 03:49:00,110] [INFO] DFAST_QC completed!
[2023-03-16 03:49:00,111] [INFO] Total running time: 0h1m27s