[2024-01-25 17:38:50,836] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:38:50,838] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:38:50,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference
[2024-01-25 17:38:51,980] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:38:51,981] [INFO] Task started: Prodigal
[2024-01-25 17:38:51,981] [INFO] Running command: gunzip -c /var/lib/cwl/stg59aa6652-39f9-4b7e-8ab3-e737b8aa0947/GCF_009711215.1_ASM971121v1_genomic.fna.gz | prodigal -d GCF_009711215.1_ASM971121v1_genomic.fna/cds.fna -a GCF_009711215.1_ASM971121v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:03,589] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:03,589] [INFO] Task started: HMMsearch
[2024-01-25 17:39:03,589] [INFO] Running command: hmmsearch --tblout GCF_009711215.1_ASM971121v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/reference_markers.hmm GCF_009711215.1_ASM971121v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:03,856] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:03,857] [INFO] Found 6/6 markers.
[2024-01-25 17:39:03,898] [INFO] Query marker FASTA was written to GCF_009711215.1_ASM971121v1_genomic.fna/markers.fasta
[2024-01-25 17:39:03,898] [INFO] Task started: Blastn
[2024-01-25 17:39:03,898] [INFO] Running command: blastn -query GCF_009711215.1_ASM971121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/reference_markers.fasta -out GCF_009711215.1_ASM971121v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:04,752] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:04,755] [INFO] Selected 23 target genomes.
[2024-01-25 17:39:04,755] [INFO] Target genome list was writen to GCF_009711215.1_ASM971121v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:04,778] [INFO] Task started: fastANI
[2024-01-25 17:39:04,778] [INFO] Running command: fastANI --query /var/lib/cwl/stg59aa6652-39f9-4b7e-8ab3-e737b8aa0947/GCF_009711215.1_ASM971121v1_genomic.fna.gz --refList GCF_009711215.1_ASM971121v1_genomic.fna/target_genomes.txt --output GCF_009711215.1_ASM971121v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:26,043] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:26,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:26,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:26,057] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:39:26,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:39:26,057] [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 laeviglucosivorans	strain=DSM 100094	GCA_900182695.1	1197861	1197861	type	True	85.6408	914	1409	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	84.5191	839	1409	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	83.8609	871	1409	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	83.8113	844	1409	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	83.5215	772	1409	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	83.4504	801	1409	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	83.2785	776	1409	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	83.228	827	1409	95	below_threshold
Paracoccus litorisediminis	strain=NBRC 112902	GCA_009711205.1	2006130	2006130	type	True	83.1726	802	1409	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	83.161	818	1409	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	82.9591	763	1409	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	82.9283	771	1409	95	below_threshold
Paracoccus denitrificans	strain=DSM 413	GCA_900100045.1	266	266	type	True	82.8145	810	1409	95	below_threshold
Paracoccus denitrificans	strain=NBRC 102528	GCA_007989485.1	266	266	type	True	82.7448	787	1409	95	below_threshold
Paracoccus ravus	strain=YJ057	GCA_004522175.1	2447760	2447760	type	True	82.2573	713	1409	95	below_threshold
Paracoccus sulfuroxidans	strain=CGMCC 1.5364	GCA_007830335.1	384678	384678	type	True	81.8565	719	1409	95	below_threshold
Paracoccus aestuariivivens	strain=NBRC 111993	GCA_009711225.1	1820333	1820333	type	True	81.6676	703	1409	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	80.7048	607	1409	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	80.1054	624	1409	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	79.8696	521	1409	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.205	519	1409	95	below_threshold
Stappia albiluteola	strain=F7233	GCA_014050225.1	2758565	2758565	type	True	76.2252	111	1409	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:26,058] [INFO] DFAST Taxonomy check result was written to GCF_009711215.1_ASM971121v1_genomic.fna/tc_result.tsv
[2024-01-25 17:39:26,059] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:26,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:26,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/checkm_data
[2024-01-25 17:39:26,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:26,100] [INFO] Task started: CheckM
[2024-01-25 17:39:26,100] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009711215.1_ASM971121v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009711215.1_ASM971121v1_genomic.fna/checkm_input GCF_009711215.1_ASM971121v1_genomic.fna/checkm_result
[2024-01-25 17:40:08,452] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:08,453] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:08,473] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:08,473] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:08,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009711215.1_ASM971121v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:08,474] [INFO] Task started: Blastn
[2024-01-25 17:40:08,474] [INFO] Running command: blastn -query GCF_009711215.1_ASM971121v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5518d208-e0be-4d26-9f3b-02fd113e59c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_009711215.1_ASM971121v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:10,130] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:10,133] [INFO] Selected 21 target genomes.
[2024-01-25 17:40:10,134] [INFO] Target genome list was writen to GCF_009711215.1_ASM971121v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:10,149] [INFO] Task started: fastANI
[2024-01-25 17:40:10,150] [INFO] Running command: fastANI --query /var/lib/cwl/stg59aa6652-39f9-4b7e-8ab3-e737b8aa0947/GCF_009711215.1_ASM971121v1_genomic.fna.gz --refList GCF_009711215.1_ASM971121v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009711215.1_ASM971121v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:29,790] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:29,802] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:29,802] [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_009711265.1	s__Paracoccus sp009711265	99.9972	1406	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900182695.1	s__Paracoccus laeviglucosivorans	85.6751	911	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711185.1	s__Paracoccus limosus	84.5187	839	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622145.1	s__Paracoccus yeei	83.8506	873	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCF_003337565.1	s__Paracoccus lutimaris	83.5287	772	1409	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	83.45	801	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001546115.1	s__Paracoccus aminovorans_B	83.204	832	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.35	95.35	0.81	0.81	2	-
GCF_000518925.1	s__Paracoccus sp000518925	83.2027	781	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_009711205.1	s__Paracoccus litorisediminis	83.1619	803	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.39	97.39	0.92	0.92	2	-
GCF_000763885.1	s__Paracoccus versutus	83.1613	818	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCF_001447385.1	s__Paracoccus sp001447385	83.0544	819	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900005615.1	s__Paracoccus aminovorans	82.9602	769	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900156255.1	s__Paracoccus thiocyanatus	82.9087	728	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	97.14	97.14	0.86	0.86	2	-
GCF_900100045.1	s__Paracoccus denitrificans	82.7941	811	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCA_018056045.1	s__Paracoccus sp018056045	82.692	482	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004522175.1	s__Paracoccus ravus	82.2497	714	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009711225.1	s__Paracoccus aestuariivivens	81.668	704	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014050225.1	s__Hongsoonwoonella albiluteola	76.2252	111	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Hongsoonwoonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425945.1	s__Brevundimonas sp001425945	75.7358	82	1409	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Caulobacterales;f__Caulobacteraceae;g__Brevundimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:40:29,803] [INFO] GTDB search result was written to GCF_009711215.1_ASM971121v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:29,804] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:29,807] [INFO] DFAST_QC result json was written to GCF_009711215.1_ASM971121v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:29,807] [INFO] DFAST_QC completed!
[2024-01-25 17:40:29,807] [INFO] Total running time: 0h1m39s