[2023-03-14 13:26:09,305] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:26:09,305] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:26:09,305] [INFO] DQC Reference Directory: /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference
[2023-03-14 13:26:11,937] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:26:11,940] [INFO] Task started: Prodigal
[2023-03-14 13:26:11,940] [INFO] Running command: cat /var/lib/cwl/stg26955ca1-a5d4-4859-abad-a3b9d3086006/OceanDNA-b32267.fa | prodigal -d OceanDNA-b32267/cds.fna -a OceanDNA-b32267/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:26:29,194] [INFO] Task succeeded: Prodigal
[2023-03-14 13:26:29,194] [INFO] Task started: HMMsearch
[2023-03-14 13:26:29,195] [INFO] Running command: hmmsearch --tblout OceanDNA-b32267/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/reference_markers.hmm OceanDNA-b32267/protein.faa > /dev/null
[2023-03-14 13:26:29,357] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:26:29,358] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg26955ca1-a5d4-4859-abad-a3b9d3086006/OceanDNA-b32267.fa]
[2023-03-14 13:26:29,373] [INFO] Query marker FASTA was written to OceanDNA-b32267/markers.fasta
[2023-03-14 13:26:29,375] [INFO] Task started: Blastn
[2023-03-14 13:26:29,375] [INFO] Running command: blastn -query OceanDNA-b32267/markers.fasta -db /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/reference_markers.fasta -out OceanDNA-b32267/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:26:29,867] [INFO] Task succeeded: Blastn
[2023-03-14 13:26:29,868] [INFO] Selected 7 target genomes.
[2023-03-14 13:26:29,868] [INFO] Target genome list was writen to OceanDNA-b32267/target_genomes.txt
[2023-03-14 13:26:29,877] [INFO] Task started: fastANI
[2023-03-14 13:26:29,877] [INFO] Running command: fastANI --query /var/lib/cwl/stg26955ca1-a5d4-4859-abad-a3b9d3086006/OceanDNA-b32267.fa --refList OceanDNA-b32267/target_genomes.txt --output OceanDNA-b32267/fastani_result.tsv --threads 1
[2023-03-14 13:26:34,342] [INFO] Task succeeded: fastANI
[2023-03-14 13:26:34,343] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:26:34,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:26:34,356] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:26:34,356] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:26:34,357] [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	82.8028	599	824	95	below_threshold
Parasphingorhabdus halotolerans	strain=JK6	GCA_012516475.1	2725558	2725558	type	True	78.2164	276	824	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	78.165	262	824	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	78.0606	318	824	95	below_threshold
Parasphingorhabdus cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	78.0454	264	824	95	below_threshold
Novosphingopyxis baekryungensis	strain=DSM 16222	GCA_000420305.1	279369	279369	type	True	76.6572	114	824	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.4501	110	824	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:26:34,357] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32267/tc_result.tsv
[2023-03-14 13:26:34,357] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:26:34,357] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:26:34,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/checkm_data
[2023-03-14 13:26:34,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:26:34,361] [INFO] Task started: CheckM
[2023-03-14 13:26:34,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32267/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32267/checkm_input OceanDNA-b32267/checkm_result
[2023-03-14 13:27:27,034] [INFO] Task succeeded: CheckM
[2023-03-14 13:27:27,035] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 56.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 13:27:27,037] [INFO] ===== Completeness check finished =====
[2023-03-14 13:27:27,037] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:27:27,037] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32267/markers.fasta)
[2023-03-14 13:27:27,038] [INFO] Task started: Blastn
[2023-03-14 13:27:27,038] [INFO] Running command: blastn -query OceanDNA-b32267/markers.fasta -db /var/lib/cwl/stg89ab618a-16b2-498a-996b-5861a702082d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32267/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:27:28,158] [INFO] Task succeeded: Blastn
[2023-03-14 13:27:28,159] [INFO] Selected 9 target genomes.
[2023-03-14 13:27:28,159] [INFO] Target genome list was writen to OceanDNA-b32267/target_genomes_gtdb.txt
[2023-03-14 13:27:28,168] [INFO] Task started: fastANI
[2023-03-14 13:27:28,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg26955ca1-a5d4-4859-abad-a3b9d3086006/OceanDNA-b32267.fa --refList OceanDNA-b32267/target_genomes_gtdb.txt --output OceanDNA-b32267/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:27:36,644] [INFO] Task succeeded: fastANI
[2023-03-14 13:27:36,650] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 13:27:36,650] [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	88.0961	563	824	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	83.21	593	824	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	83.1732	583	824	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	82.837	602	824	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	82.7889	600	824	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	82.6042	574	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067055.1	s__Parasphingorhabdus sp018067055	82.054	353	824	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	81.8617	551	824	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	81.8392	452	824	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
--------------------------------------------------------------------------------
[2023-03-14 13:27:36,650] [INFO] GTDB search result was written to OceanDNA-b32267/result_gtdb.tsv
[2023-03-14 13:27:36,650] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:27:36,651] [INFO] DFAST_QC result json was written to OceanDNA-b32267/dqc_result.json
[2023-03-14 13:27:36,651] [INFO] DFAST_QC completed!
[2023-03-14 13:27:36,651] [INFO] Total running time: 0h1m27s