[2023-03-14 14:16:15,391] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:16:15,392] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:16:15,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference
[2023-03-14 14:16:16,459] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:16:16,460] [INFO] Task started: Prodigal
[2023-03-14 14:16:16,460] [INFO] Running command: cat /var/lib/cwl/stg77cccb4b-16fd-4ad6-ab5a-b56878c52310/OceanDNA-b29593.fa | prodigal -d OceanDNA-b29593/cds.fna -a OceanDNA-b29593/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:16:29,120] [INFO] Task succeeded: Prodigal
[2023-03-14 14:16:29,120] [INFO] Task started: HMMsearch
[2023-03-14 14:16:29,120] [INFO] Running command: hmmsearch --tblout OceanDNA-b29593/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/reference_markers.hmm OceanDNA-b29593/protein.faa > /dev/null
[2023-03-14 14:16:29,494] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:16:29,494] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg77cccb4b-16fd-4ad6-ab5a-b56878c52310/OceanDNA-b29593.fa]
[2023-03-14 14:16:29,525] [INFO] Query marker FASTA was written to OceanDNA-b29593/markers.fasta
[2023-03-14 14:16:29,529] [INFO] Task started: Blastn
[2023-03-14 14:16:29,529] [INFO] Running command: blastn -query OceanDNA-b29593/markers.fasta -db /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/reference_markers.fasta -out OceanDNA-b29593/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:16:30,951] [INFO] Task succeeded: Blastn
[2023-03-14 14:16:30,953] [INFO] Selected 13 target genomes.
[2023-03-14 14:16:30,953] [INFO] Target genome list was writen to OceanDNA-b29593/target_genomes.txt
[2023-03-14 14:16:30,958] [INFO] Task started: fastANI
[2023-03-14 14:16:30,958] [INFO] Running command: fastANI --query /var/lib/cwl/stg77cccb4b-16fd-4ad6-ab5a-b56878c52310/OceanDNA-b29593.fa --refList OceanDNA-b29593/target_genomes.txt --output OceanDNA-b29593/fastani_result.tsv --threads 1
[2023-03-14 14:16:45,704] [INFO] Task succeeded: fastANI
[2023-03-14 14:16:45,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:16:45,705] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:16:45,714] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:16:45,714] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 14:16:45,714] [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
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	80.9866	401	624	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	80.9829	390	624	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	80.5281	372	624	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	80.4061	360	624	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	80.3508	337	624	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	80.3187	340	624	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.3072	353	624	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	80.0571	341	624	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	79.9126	347	624	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	79.8277	350	624	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.7449	359	624	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	79.7415	333	624	95	below_threshold
Paracoccus amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	78.6547	264	624	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 14:16:45,715] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29593/tc_result.tsv
[2023-03-14 14:16:45,716] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:16:45,716] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:16:45,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/checkm_data
[2023-03-14 14:16:45,716] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:16:45,730] [INFO] Task started: CheckM
[2023-03-14 14:16:45,730] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29593/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29593/checkm_input OceanDNA-b29593/checkm_result
[2023-03-14 14:17:35,423] [INFO] Task succeeded: CheckM
[2023-03-14 14:17:35,424] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:17:35,426] [INFO] ===== Completeness check finished =====
[2023-03-14 14:17:35,427] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:17:35,427] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29593/markers.fasta)
[2023-03-14 14:17:35,428] [INFO] Task started: Blastn
[2023-03-14 14:17:35,428] [INFO] Running command: blastn -query OceanDNA-b29593/markers.fasta -db /var/lib/cwl/stg87042890-355e-476d-aa1a-eff6ebf3ce3a/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29593/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:17:36,203] [INFO] Task succeeded: Blastn
[2023-03-14 14:17:36,204] [INFO] Selected 11 target genomes.
[2023-03-14 14:17:36,204] [INFO] Target genome list was writen to OceanDNA-b29593/target_genomes_gtdb.txt
[2023-03-14 14:17:36,242] [INFO] Task started: fastANI
[2023-03-14 14:17:36,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg77cccb4b-16fd-4ad6-ab5a-b56878c52310/OceanDNA-b29593.fa --refList OceanDNA-b29593/target_genomes_gtdb.txt --output OceanDNA-b29593/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:17:44,804] [INFO] Task succeeded: fastANI
[2023-03-14 14:17:44,811] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:17:44,812] [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_002294185.1	s__Paracoccus sp002294185	83.1716	425	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_018860165.1	s__Paracoccus sp018860165	81.0331	386	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	81.0096	400	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900111675.1	s__Paracoccus homiensis	80.5124	373	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	80.4123	381	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_900110285.1	s__Paracoccus alcaliphilus	80.4061	360	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708075.1	s__Paracoccus lichenicola	80.3192	340	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017315735.1	s__Paracoccus sp017315735	80.3072	353	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014656455.1	s__Paracoccus aerius	79.8277	350	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
GCF_003259195.1	s__Paracoccus sediminilitoris	79.7264	334	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_007096355.1	s__Paracoccus sp007096355	79.4148	347	624	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:17:44,812] [INFO] GTDB search result was written to OceanDNA-b29593/result_gtdb.tsv
[2023-03-14 14:17:44,812] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:17:44,813] [INFO] DFAST_QC result json was written to OceanDNA-b29593/dqc_result.json
[2023-03-14 14:17:44,813] [INFO] DFAST_QC completed!
[2023-03-14 14:17:44,814] [INFO] Total running time: 0h1m29s