[2024-01-24 11:35:23,306] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,308] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,309] [INFO] DQC Reference Directory: /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference
[2024-01-24 11:35:26,243] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,244] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,244] [INFO] Running command: gunzip -c /var/lib/cwl/stg07ca26db-1ae3-41d9-971b-9416f4fb441b/GCF_028553765.1_ASM2855376v1_genomic.fna.gz | prodigal -d GCF_028553765.1_ASM2855376v1_genomic.fna/cds.fna -a GCF_028553765.1_ASM2855376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:37,143] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:37,143] [INFO] Task started: HMMsearch
[2024-01-24 11:35:37,143] [INFO] Running command: hmmsearch --tblout GCF_028553765.1_ASM2855376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/reference_markers.hmm GCF_028553765.1_ASM2855376v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:37,485] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:37,486] [INFO] Found 6/6 markers.
[2024-01-24 11:35:37,521] [INFO] Query marker FASTA was written to GCF_028553765.1_ASM2855376v1_genomic.fna/markers.fasta
[2024-01-24 11:35:37,521] [INFO] Task started: Blastn
[2024-01-24 11:35:37,521] [INFO] Running command: blastn -query GCF_028553765.1_ASM2855376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/reference_markers.fasta -out GCF_028553765.1_ASM2855376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:38,536] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:38,539] [INFO] Selected 18 target genomes.
[2024-01-24 11:35:38,540] [INFO] Target genome list was writen to GCF_028553765.1_ASM2855376v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:38,547] [INFO] Task started: fastANI
[2024-01-24 11:35:38,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ca26db-1ae3-41d9-971b-9416f4fb441b/GCF_028553765.1_ASM2855376v1_genomic.fna.gz --refList GCF_028553765.1_ASM2855376v1_genomic.fna/target_genomes.txt --output GCF_028553765.1_ASM2855376v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:53,121] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:53,122] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:53,122] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:53,136] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:53,136] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:53,137] [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=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	83.4178	693	1213	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	83.3909	744	1213	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	83.2129	717	1213	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	82.696	713	1213	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.3641	652	1213	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	82.3379	657	1213	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	82.2954	616	1213	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	82.0697	628	1213	95	below_threshold
Paracoccus sediminis	strain=CMB17	GCA_004310385.1	1214787	1214787	type	True	82.0639	631	1213	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	81.9432	644	1213	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	81.9185	635	1213	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	81.8732	641	1213	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	81.7391	634	1213	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.7121	593	1213	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	81.3763	640	1213	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	80.8495	614	1213	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	80.5322	600	1213	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	80.4279	611	1213	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:53,139] [INFO] DFAST Taxonomy check result was written to GCF_028553765.1_ASM2855376v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:53,139] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:53,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:53,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/checkm_data
[2024-01-24 11:35:53,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:53,177] [INFO] Task started: CheckM
[2024-01-24 11:35:53,177] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028553765.1_ASM2855376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028553765.1_ASM2855376v1_genomic.fna/checkm_input GCF_028553765.1_ASM2855376v1_genomic.fna/checkm_result
[2024-01-24 11:36:40,069] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:40,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:40,093] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:40,093] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:40,094] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028553765.1_ASM2855376v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:40,094] [INFO] Task started: Blastn
[2024-01-24 11:36:40,094] [INFO] Running command: blastn -query GCF_028553765.1_ASM2855376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3845503f-59ae-423b-81d0-ea0cece4a67e/dqc_reference/reference_markers_gtdb.fasta -out GCF_028553765.1_ASM2855376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:42,038] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:42,044] [INFO] Selected 14 target genomes.
[2024-01-24 11:36:42,044] [INFO] Target genome list was writen to GCF_028553765.1_ASM2855376v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:42,088] [INFO] Task started: fastANI
[2024-01-24 11:36:42,089] [INFO] Running command: fastANI --query /var/lib/cwl/stg07ca26db-1ae3-41d9-971b-9416f4fb441b/GCF_028553765.1_ASM2855376v1_genomic.fna.gz --refList GCF_028553765.1_ASM2855376v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028553765.1_ASM2855376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:54,388] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:54,399] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:36:54,400] [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_017744015.1	s__Paracoccus sp002732665	83.9264	750	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_018860165.1	s__Paracoccus sp018860165	83.9078	766	1213	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	83.3462	748	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_002294185.1	s__Paracoccus sp002294185	83.1479	660	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_900111675.1	s__Paracoccus homiensis	82.6871	715	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631945.1	s__Paracoccus haematequi	82.6825	676	1213	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	82.3525	653	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110285.1	s__Paracoccus alcaliphilus	82.291	661	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594815.1	s__Paracoccus aestuarii	82.2802	617	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000787695.1	s__Paracoccus sp000787695	81.8229	582	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003007735.2	s__Paracoccus marinus_A	81.5952	635	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003255745.1	s__Paracoccus saliphilus_A	81.3247	608	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	80.9795	629	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_900199195.1	s__Paracoccus seriniphilus	80.5393	600	1213	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:54,401] [INFO] GTDB search result was written to GCF_028553765.1_ASM2855376v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:54,402] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:54,406] [INFO] DFAST_QC result json was written to GCF_028553765.1_ASM2855376v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:54,406] [INFO] DFAST_QC completed!
[2024-01-24 11:36:54,406] [INFO] Total running time: 0h1m31s