[2024-01-25 19:02:05,642] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:02:05,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:02:05,644] [INFO] DQC Reference Directory: /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference
[2024-01-25 19:02:06,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:02:06,818] [INFO] Task started: Prodigal
[2024-01-25 19:02:06,818] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7c2d61b-7635-4a4a-a866-762768b03393/GCF_000420145.1_ASM42014v1_genomic.fna.gz | prodigal -d GCF_000420145.1_ASM42014v1_genomic.fna/cds.fna -a GCF_000420145.1_ASM42014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:02:14,660] [INFO] Task succeeded: Prodigal
[2024-01-25 19:02:14,660] [INFO] Task started: HMMsearch
[2024-01-25 19:02:14,660] [INFO] Running command: hmmsearch --tblout GCF_000420145.1_ASM42014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/reference_markers.hmm GCF_000420145.1_ASM42014v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:02:14,869] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:02:14,870] [INFO] Found 6/6 markers.
[2024-01-25 19:02:14,897] [INFO] Query marker FASTA was written to GCF_000420145.1_ASM42014v1_genomic.fna/markers.fasta
[2024-01-25 19:02:14,897] [INFO] Task started: Blastn
[2024-01-25 19:02:14,897] [INFO] Running command: blastn -query GCF_000420145.1_ASM42014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/reference_markers.fasta -out GCF_000420145.1_ASM42014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:02:15,885] [INFO] Task succeeded: Blastn
[2024-01-25 19:02:15,888] [INFO] Selected 19 target genomes.
[2024-01-25 19:02:15,888] [INFO] Target genome list was writen to GCF_000420145.1_ASM42014v1_genomic.fna/target_genomes.txt
[2024-01-25 19:02:15,917] [INFO] Task started: fastANI
[2024-01-25 19:02:15,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c2d61b-7635-4a4a-a866-762768b03393/GCF_000420145.1_ASM42014v1_genomic.fna.gz --refList GCF_000420145.1_ASM42014v1_genomic.fna/target_genomes.txt --output GCF_000420145.1_ASM42014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:02:31,265] [INFO] Task succeeded: fastANI
[2024-01-25 19:02:31,265] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:02:31,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:02:31,276] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:02:31,277] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:02:31,277] [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 zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	100.0	997	999	95	conclusive
Paracoccus liaowanqingii	strain=2251	GCA_004683865.2	2560053	2560053	type	True	84.1597	724	999	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	84.0642	651	999	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	83.7247	729	999	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	83.6803	721	999	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	83.2367	723	999	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	82.9626	652	999	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	82.9026	685	999	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	82.8362	635	999	95	below_threshold
Paracoccus tibetensis	strain=CGMCC 1.8925	GCA_900102505.1	336292	336292	type	True	82.7756	668	999	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	82.5766	624	999	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	82.3449	688	999	95	below_threshold
Paracoccus fontiphilus	strain=MVW-1	GCA_017356265.1	1815556	1815556	type	True	82.3182	626	999	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	82.2986	600	999	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_016757275.1	1915382	1915382	type	True	82.078	619	999	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	82.0418	618	999	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	81.2792	563	999	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.1024	587	999	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.3131	476	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:02:31,278] [INFO] DFAST Taxonomy check result was written to GCF_000420145.1_ASM42014v1_genomic.fna/tc_result.tsv
[2024-01-25 19:02:31,279] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:02:31,279] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:02:31,279] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/checkm_data
[2024-01-25 19:02:31,280] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:02:31,312] [INFO] Task started: CheckM
[2024-01-25 19:02:31,313] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000420145.1_ASM42014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000420145.1_ASM42014v1_genomic.fna/checkm_input GCF_000420145.1_ASM42014v1_genomic.fna/checkm_result
[2024-01-25 19:03:05,260] [INFO] Task succeeded: CheckM
[2024-01-25 19:03:05,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:03:05,284] [INFO] ===== Completeness check finished =====
[2024-01-25 19:03:05,284] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:03:05,285] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000420145.1_ASM42014v1_genomic.fna/markers.fasta)
[2024-01-25 19:03:05,285] [INFO] Task started: Blastn
[2024-01-25 19:03:05,285] [INFO] Running command: blastn -query GCF_000420145.1_ASM42014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfd2af7c3-86df-456c-aac6-0faaa186db48/dqc_reference/reference_markers_gtdb.fasta -out GCF_000420145.1_ASM42014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:03:07,214] [INFO] Task succeeded: Blastn
[2024-01-25 19:03:07,217] [INFO] Selected 15 target genomes.
[2024-01-25 19:03:07,217] [INFO] Target genome list was writen to GCF_000420145.1_ASM42014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:03:07,249] [INFO] Task started: fastANI
[2024-01-25 19:03:07,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7c2d61b-7635-4a4a-a866-762768b03393/GCF_000420145.1_ASM42014v1_genomic.fna.gz --refList GCF_000420145.1_ASM42014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000420145.1_ASM42014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:03:21,132] [INFO] Task succeeded: fastANI
[2024-01-25 19:03:21,143] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:03:21,144] [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_000420145.1	s__Paracoccus zeaxanthinifaciens	100.0	997	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018860625.1	s__Paracoccus sp018860625	90.1901	868	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004683865.2	s__Paracoccus liaowanqingii	84.159	725	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.54	96.54	0.86	0.86	2	-
GCF_003594815.1	s__Paracoccus aestuarii	84.0518	652	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048225.1	s__Paracoccus gahaiensis	83.8005	722	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006151785.1	s__Paracoccus marcusii	83.7883	666	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.50	96.78	0.86	0.75	9	-
GCF_003056335.1	s__Paracoccus indicus	83.7535	727	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005048265.1	s__Paracoccus hibiscisoli	83.6643	723	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_003259195.1	s__Paracoccus sediminilitoris	83.2487	722	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_900111675.1	s__Paracoccus homiensis	82.9401	655	999	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	82.9331	683	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_900102505.1	s__Paracoccus tibetensis	82.7613	670	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017356265.1	s__Paracoccus fontiphilus	82.313	626	999	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	82.2036	612	999	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	82.0452	618	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.01	98.03	0.91	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-25 19:03:21,146] [INFO] GTDB search result was written to GCF_000420145.1_ASM42014v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:03:21,147] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:03:21,151] [INFO] DFAST_QC result json was written to GCF_000420145.1_ASM42014v1_genomic.fna/dqc_result.json
[2024-01-25 19:03:21,151] [INFO] DFAST_QC completed!
[2024-01-25 19:03:21,151] [INFO] Total running time: 0h1m16s