[2023-03-18 10:37:58,274] [INFO] DFAST_QC pipeline started.
[2023-03-18 10:37:58,274] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 10:37:58,274] [INFO] DQC Reference Directory: /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference
[2023-03-18 10:37:59,405] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 10:37:59,405] [INFO] Task started: Prodigal
[2023-03-18 10:37:59,405] [INFO] Running command: cat /var/lib/cwl/stgb975195f-6931-4774-87d7-0b62e29c8894/OceanDNA-b32285.fa | prodigal -d OceanDNA-b32285/cds.fna -a OceanDNA-b32285/protein.faa -g 11 -q > /dev/null
[2023-03-18 10:38:14,161] [INFO] Task succeeded: Prodigal
[2023-03-18 10:38:14,162] [INFO] Task started: HMMsearch
[2023-03-18 10:38:14,162] [INFO] Running command: hmmsearch --tblout OceanDNA-b32285/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/reference_markers.hmm OceanDNA-b32285/protein.faa > /dev/null
[2023-03-18 10:38:14,335] [INFO] Task succeeded: HMMsearch
[2023-03-18 10:38:14,336] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb975195f-6931-4774-87d7-0b62e29c8894/OceanDNA-b32285.fa]
[2023-03-18 10:38:14,351] [INFO] Query marker FASTA was written to OceanDNA-b32285/markers.fasta
[2023-03-18 10:38:14,352] [INFO] Task started: Blastn
[2023-03-18 10:38:14,352] [INFO] Running command: blastn -query OceanDNA-b32285/markers.fasta -db /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/reference_markers.fasta -out OceanDNA-b32285/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:38:14,965] [INFO] Task succeeded: Blastn
[2023-03-18 10:38:14,965] [INFO] Selected 16 target genomes.
[2023-03-18 10:38:14,966] [INFO] Target genome list was writen to OceanDNA-b32285/target_genomes.txt
[2023-03-18 10:38:14,974] [INFO] Task started: fastANI
[2023-03-18 10:38:14,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgb975195f-6931-4774-87d7-0b62e29c8894/OceanDNA-b32285.fa --refList OceanDNA-b32285/target_genomes.txt --output OceanDNA-b32285/fastani_result.tsv --threads 1
[2023-03-18 10:38:23,998] [INFO] Task succeeded: fastANI
[2023-03-18 10:38:23,999] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 10:38:23,999] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 10:38:24,005] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 10:38:24,005] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 10:38:24,005] [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 cellanae	strain=JHSY0214	GCA_017498565.1	2806553	2806553	type	True	79.9556	414	797	95	below_threshold
Parasphingorhabdus litoris	strain=DSM 22379	GCA_020906275.1	394733	394733	type	True	79.4492	398	797	95	below_threshold
Parasphingorhabdus flavimaris	strain=SW-151	GCA_013371215.1	266812	266812	type	True	78.0825	229	797	95	below_threshold
Parasphingorhabdus marina	strain=DSM 22363	GCA_900128895.1	394732	394732	type	True	77.6707	209	797	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	76.2598	60	797	95	below_threshold
Sphingorhabdus pulchriflava	strain=GY_G	GCA_003367235.1	2292257	2292257	type	True	76.2026	54	797	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	76.0318	56	797	95	below_threshold
Sphingorhabdus contaminans	strain=KCTC32445	GCA_007280415.1	1343899	1343899	type	True	75.9044	50	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 10:38:24,005] [INFO] DFAST Taxonomy check result was written to OceanDNA-b32285/tc_result.tsv
[2023-03-18 10:38:24,006] [INFO] ===== Taxonomy check completed =====
[2023-03-18 10:38:24,006] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 10:38:24,006] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/checkm_data
[2023-03-18 10:38:24,006] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 10:38:24,266] [INFO] Task started: CheckM
[2023-03-18 10:38:24,267] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b32285/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b32285/checkm_input OceanDNA-b32285/checkm_result
[2023-03-18 10:39:04,028] [INFO] Task succeeded: CheckM
[2023-03-18 10:39:04,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 10:39:04,032] [INFO] ===== Completeness check finished =====
[2023-03-18 10:39:04,032] [INFO] ===== Start GTDB Search =====
[2023-03-18 10:39:04,033] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b32285/markers.fasta)
[2023-03-18 10:39:04,034] [INFO] Task started: Blastn
[2023-03-18 10:39:04,034] [INFO] Running command: blastn -query OceanDNA-b32285/markers.fasta -db /var/lib/cwl/stg696632a5-864f-4b61-973f-c5ad67c56661/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b32285/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 10:39:05,077] [INFO] Task succeeded: Blastn
[2023-03-18 10:39:05,078] [INFO] Selected 14 target genomes.
[2023-03-18 10:39:05,079] [INFO] Target genome list was writen to OceanDNA-b32285/target_genomes_gtdb.txt
[2023-03-18 10:39:05,129] [INFO] Task started: fastANI
[2023-03-18 10:39:05,129] [INFO] Running command: fastANI --query /var/lib/cwl/stgb975195f-6931-4774-87d7-0b62e29c8894/OceanDNA-b32285.fa --refList OceanDNA-b32285/target_genomes_gtdb.txt --output OceanDNA-b32285/fastani_result_gtdb.tsv --threads 1
[2023-03-18 10:39:14,161] [INFO] Task succeeded: fastANI
[2023-03-18 10:39:14,169] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 10:39:14,170] [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_017498565.1	s__Parasphingorhabdus sp017498565	79.9556	414	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258045.1	s__Parasphingorhabdus sp900258045	79.7935	423	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900149705.1	s__Parasphingorhabdus sp900149705	79.7261	393	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015478735.1	s__Parasphingorhabdus sp015478735	79.0046	284	797	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	78.4439	248	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650955.1	s__Parasphingorhabdus sp001650955	78.1977	216	797	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	78.1596	247	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	97.08	97.08	0.87	0.87	2	-
GCF_013371215.1	s__Parasphingorhabdus flavimaris	78.0663	230	797	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	77.9906	210	797	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	77.935	219	797	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	77.9246	183	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	99.83	99.79	0.95	0.93	9	-
GCF_902506555.1	s__Parasphingorhabdus sp902506555	77.8863	232	797	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	77.7624	232	797	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Parasphingorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 10:39:14,171] [INFO] GTDB search result was written to OceanDNA-b32285/result_gtdb.tsv
[2023-03-18 10:39:14,172] [INFO] ===== GTDB Search completed =====
[2023-03-18 10:39:14,176] [INFO] DFAST_QC result json was written to OceanDNA-b32285/dqc_result.json
[2023-03-18 10:39:14,176] [INFO] DFAST_QC completed!
[2023-03-18 10:39:14,176] [INFO] Total running time: 0h1m16s