[2023-03-16 04:54:07,050] [INFO] DFAST_QC pipeline started.
[2023-03-16 04:54:07,050] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 04:54:07,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference
[2023-03-16 04:54:08,310] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 04:54:08,311] [INFO] Task started: Prodigal
[2023-03-16 04:54:08,311] [INFO] Running command: cat /var/lib/cwl/stgead019b4-3189-4ad0-85e1-d8ed6c0f8030/OceanDNA-b26695.fa | prodigal -d OceanDNA-b26695/cds.fna -a OceanDNA-b26695/protein.faa -g 11 -q > /dev/null
[2023-03-16 04:54:19,564] [INFO] Task succeeded: Prodigal
[2023-03-16 04:54:19,564] [INFO] Task started: HMMsearch
[2023-03-16 04:54:19,564] [INFO] Running command: hmmsearch --tblout OceanDNA-b26695/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/reference_markers.hmm OceanDNA-b26695/protein.faa > /dev/null
[2023-03-16 04:54:19,805] [INFO] Task succeeded: HMMsearch
[2023-03-16 04:54:19,805] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgead019b4-3189-4ad0-85e1-d8ed6c0f8030/OceanDNA-b26695.fa]
[2023-03-16 04:54:19,825] [INFO] Query marker FASTA was written to OceanDNA-b26695/markers.fasta
[2023-03-16 04:54:19,825] [INFO] Task started: Blastn
[2023-03-16 04:54:19,825] [INFO] Running command: blastn -query OceanDNA-b26695/markers.fasta -db /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/reference_markers.fasta -out OceanDNA-b26695/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:54:20,495] [INFO] Task succeeded: Blastn
[2023-03-16 04:54:20,495] [INFO] Selected 19 target genomes.
[2023-03-16 04:54:20,496] [INFO] Target genome list was writen to OceanDNA-b26695/target_genomes.txt
[2023-03-16 04:54:20,508] [INFO] Task started: fastANI
[2023-03-16 04:54:20,509] [INFO] Running command: fastANI --query /var/lib/cwl/stgead019b4-3189-4ad0-85e1-d8ed6c0f8030/OceanDNA-b26695.fa --refList OceanDNA-b26695/target_genomes.txt --output OceanDNA-b26695/fastani_result.tsv --threads 1
[2023-03-16 04:54:37,153] [INFO] Task succeeded: fastANI
[2023-03-16 04:54:37,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 04:54:37,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 04:54:37,165] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 04:54:37,165] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 04:54:37,165] [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
Devosia insulae	strain=DS-56	GCA_000970465.2	408174	408174	type	True	79.3577	372	626	95	below_threshold
Devosia geojensis	strain=BD-c194	GCA_000969415.1	443610	443610	type	True	78.6942	294	626	95	below_threshold
Devosia enhydra	strain=ATCC 23634	GCA_900119845.1	665118	665118	type	True	78.6261	258	626	95	below_threshold
Youhaiella tibetensis	strain=fig4	GCA_008000755.1	1447062	1447062	type	True	78.3793	273	626	95	below_threshold
Youhaiella tibetensis	strain=CGMCC 1.12719	GCA_014638565.1	1447062	1447062	type	True	78.3434	285	626	95	below_threshold
Arsenicitalea aurantiaca	strain=42-50	GCA_003994485.1	1783274	1783274	type	True	78.2628	221	626	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	78.2044	265	626	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	78.1606	246	626	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_900128975.1	288995	288995	type	True	77.8457	222	626	95	below_threshold
Devosia limi	strain=DSM 17137	GCA_000970435.1	288995	288995	type	True	77.8442	218	626	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	77.3397	151	626	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	77.1668	187	626	95	below_threshold
Devosia pacifica	strain=KCTC 32437	GCA_014652635.1	1335967	1335967	type	True	77.1074	140	626	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	77.0709	160	626	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3568	149	626	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	76.1417	99	626	95	below_threshold
Methylorubrum suomiense	strain=DSM 14458	GCA_022179765.1	144191	144191	type	True	76.1134	105	626	95	below_threshold
Bradyrhizobium cajani	strain=1010	GCA_009759665.1	1928661	1928661	type	True	76.1105	124	626	95	below_threshold
Methylobacterium longum	strain=DSM 23933	GCA_022179385.1	767694	767694	type	True	75.8578	106	626	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 04:54:37,165] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26695/tc_result.tsv
[2023-03-16 04:54:37,165] [INFO] ===== Taxonomy check completed =====
[2023-03-16 04:54:37,166] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 04:54:37,166] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/checkm_data
[2023-03-16 04:54:37,166] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 04:54:37,174] [INFO] Task started: CheckM
[2023-03-16 04:54:37,174] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26695/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26695/checkm_input OceanDNA-b26695/checkm_result
[2023-03-16 04:55:08,887] [INFO] Task succeeded: CheckM
[2023-03-16 04:55:08,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.67%
Contamintation: 4.69%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-16 04:55:08,890] [INFO] ===== Completeness check finished =====
[2023-03-16 04:55:08,890] [INFO] ===== Start GTDB Search =====
[2023-03-16 04:55:08,890] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26695/markers.fasta)
[2023-03-16 04:55:08,891] [INFO] Task started: Blastn
[2023-03-16 04:55:08,891] [INFO] Running command: blastn -query OceanDNA-b26695/markers.fasta -db /var/lib/cwl/stgc3679319-ca34-40d2-af36-43748daecb54/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26695/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 04:55:09,951] [INFO] Task succeeded: Blastn
[2023-03-16 04:55:09,952] [INFO] Selected 15 target genomes.
[2023-03-16 04:55:09,952] [INFO] Target genome list was writen to OceanDNA-b26695/target_genomes_gtdb.txt
[2023-03-16 04:55:09,968] [INFO] Task started: fastANI
[2023-03-16 04:55:09,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgead019b4-3189-4ad0-85e1-d8ed6c0f8030/OceanDNA-b26695.fa --refList OceanDNA-b26695/target_genomes_gtdb.txt --output OceanDNA-b26695/fastani_result_gtdb.tsv --threads 1
[2023-03-16 04:55:21,502] [INFO] Task succeeded: fastANI
[2023-03-16 04:55:21,511] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 04:55:21,512] [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_017307495.1	s__Devosia_A sp017307495	79.8034	355	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	98.70	98.70	0.95	0.95	2	-
GCF_014873135.1	s__Devosia_A sp014873135	79.6721	364	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899085.1	s__Devosia_A sp001899085	79.6492	380	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	99.98	99.97	0.99	0.99	3	-
GCA_016713105.1	s__Devosia_A sp016713105	79.6407	364	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001402915.1	s__Devosia_A sp001402915	79.6149	375	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899075.1	s__Devosia_A sp001899075	79.4848	351	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016213505.1	s__Devosia_A nanyangense	79.3478	334	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425235.1	s__Devosia_A sp001425235	79.2455	382	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	97.96	97.96	0.95	0.95	2	-
GCA_903842455.1	s__Devosia_A sp903842455	79.0484	348	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015657675.1	s__Devosia_A sp015657675	78.9136	329	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144345.1	s__Devosia_A sp004144345	78.826	319	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969415.1	s__Devosia geojensis	78.7232	292	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900119845.1	s__Devosia_A enhydra	78.6006	260	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828145.1	s__Devosia sp018828145	78.3515	270	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	99.99	99.98	0.99	0.98	4	-
GCF_014837245.1	s__Devosia sp014837245	78.2941	194	626	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 04:55:21,512] [INFO] GTDB search result was written to OceanDNA-b26695/result_gtdb.tsv
[2023-03-16 04:55:21,513] [INFO] ===== GTDB Search completed =====
[2023-03-16 04:55:21,514] [INFO] DFAST_QC result json was written to OceanDNA-b26695/dqc_result.json
[2023-03-16 04:55:21,515] [INFO] DFAST_QC completed!
[2023-03-16 04:55:21,515] [INFO] Total running time: 0h1m14s