[2024-01-25 19:45:35,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:35,522] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:35,522] [INFO] DQC Reference Directory: /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference
[2024-01-25 19:45:36,683] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:36,684] [INFO] Task started: Prodigal
[2024-01-25 19:45:36,684] [INFO] Running command: gunzip -c /var/lib/cwl/stgb85e5c1f-f808-4dcc-9068-681b8b0546f4/GCF_011308835.1_ASM1130883v1_genomic.fna.gz | prodigal -d GCF_011308835.1_ASM1130883v1_genomic.fna/cds.fna -a GCF_011308835.1_ASM1130883v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:46,419] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:46,419] [INFO] Task started: HMMsearch
[2024-01-25 19:45:46,419] [INFO] Running command: hmmsearch --tblout GCF_011308835.1_ASM1130883v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/reference_markers.hmm GCF_011308835.1_ASM1130883v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:46,637] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:46,639] [INFO] Found 6/6 markers.
[2024-01-25 19:45:46,669] [INFO] Query marker FASTA was written to GCF_011308835.1_ASM1130883v1_genomic.fna/markers.fasta
[2024-01-25 19:45:46,669] [INFO] Task started: Blastn
[2024-01-25 19:45:46,669] [INFO] Running command: blastn -query GCF_011308835.1_ASM1130883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/reference_markers.fasta -out GCF_011308835.1_ASM1130883v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:47,570] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:47,573] [INFO] Selected 21 target genomes.
[2024-01-25 19:45:47,573] [INFO] Target genome list was writen to GCF_011308835.1_ASM1130883v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:47,586] [INFO] Task started: fastANI
[2024-01-25 19:45:47,587] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85e5c1f-f808-4dcc-9068-681b8b0546f4/GCF_011308835.1_ASM1130883v1_genomic.fna.gz --refList GCF_011308835.1_ASM1130883v1_genomic.fna/target_genomes.txt --output GCF_011308835.1_ASM1130883v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:46:03,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:03,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:46:03,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:46:03,763] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:46:03,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:46:03,763] [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 xiamenensis	strain=12-3	GCA_011308835.1	2714901	2714901	type	True	100.0	1203	1204	95	conclusive
Paracoccus aurantiacus	strain=TK008	GCA_007993065.1	2599412	2599412	type	True	82.6991	734	1204	95	below_threshold
Paracoccus jeotgali	strain=CBA4604	GCA_002865605.1	2065379	2065379	type	True	82.1906	666	1204	95	below_threshold
Paracoccus isoporae	strain=DSM 22220	GCA_900101865.1	591205	591205	type	True	81.61	691	1204	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	80.41	605	1204	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	80.1995	587	1204	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	80.0844	614	1204	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_003633525.1	82367	82367	type	True	79.9958	580	1204	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.9908	577	1204	95	below_threshold
Paracoccus halophilus	strain=JCM 14014	GCA_000763905.1	376733	376733	type	True	79.9405	573	1204	95	below_threshold
Paracoccus pantotrophus	strain=DSM 2944	GCA_008824185.1	82367	82367	type	True	79.8579	587	1204	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	79.737	488	1204	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.7163	528	1204	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	79.5454	515	1204	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	79.4884	481	1204	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.4558	500	1204	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.4345	488	1204	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.3402	446	1204	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.3373	520	1204	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.3295	529	1204	95	below_threshold
Paracoccus bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	78.9684	464	1204	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:46:03,764] [INFO] DFAST Taxonomy check result was written to GCF_011308835.1_ASM1130883v1_genomic.fna/tc_result.tsv
[2024-01-25 19:46:03,765] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:46:03,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:46:03,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/checkm_data
[2024-01-25 19:46:03,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:46:03,808] [INFO] Task started: CheckM
[2024-01-25 19:46:03,808] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011308835.1_ASM1130883v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011308835.1_ASM1130883v1_genomic.fna/checkm_input GCF_011308835.1_ASM1130883v1_genomic.fna/checkm_result
[2024-01-25 19:46:37,470] [INFO] Task succeeded: CheckM
[2024-01-25 19:46:37,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:46:37,500] [INFO] ===== Completeness check finished =====
[2024-01-25 19:46:37,501] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:46:37,501] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011308835.1_ASM1130883v1_genomic.fna/markers.fasta)
[2024-01-25 19:46:37,501] [INFO] Task started: Blastn
[2024-01-25 19:46:37,501] [INFO] Running command: blastn -query GCF_011308835.1_ASM1130883v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg40ad81eb-d758-404c-886a-043a4b02076d/dqc_reference/reference_markers_gtdb.fasta -out GCF_011308835.1_ASM1130883v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:39,300] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:39,303] [INFO] Selected 14 target genomes.
[2024-01-25 19:46:39,303] [INFO] Target genome list was writen to GCF_011308835.1_ASM1130883v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:46:39,330] [INFO] Task started: fastANI
[2024-01-25 19:46:39,330] [INFO] Running command: fastANI --query /var/lib/cwl/stgb85e5c1f-f808-4dcc-9068-681b8b0546f4/GCF_011308835.1_ASM1130883v1_genomic.fna.gz --refList GCF_011308835.1_ASM1130883v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011308835.1_ASM1130883v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:51,456] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:51,465] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:51,466] [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_011308835.1	s__Paracoccus xiamenensis	100.0	1203	1204	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_013868135.1	s__Paracoccus sp013868135	86.0225	885	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007993065.1	s__Paracoccus aurantiacus	82.6918	734	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002865605.1	s__Paracoccus jeotgali	82.2026	665	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.34	96.34	0.97	0.97	2	-
GCF_900101865.1	s__Paracoccus isoporae	81.6015	691	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005768755.1	s__Paracoccus denitrificans_B	81.5411	705	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337565.1	s__Paracoccus lutimaris	80.4479	601	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018056045.1	s__Paracoccus sp018056045	80.2425	385	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007096355.1	s__Paracoccus sp007096355	80.1063	572	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	80.0293	572	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008824185.1	s__Paracoccus pantotrophus	79.8648	585	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.22	98.98	0.90	0.84	8	-
GCF_017315735.1	s__Paracoccus sp017315735	79.7462	525	1204	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	79.1601	436	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452815.1	s__UBA6796 sp002452815	78.552	412	1204	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:51,467] [INFO] GTDB search result was written to GCF_011308835.1_ASM1130883v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:51,468] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:51,471] [INFO] DFAST_QC result json was written to GCF_011308835.1_ASM1130883v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:51,471] [INFO] DFAST_QC completed!
[2024-01-25 19:46:51,471] [INFO] Total running time: 0h1m16s