[2024-01-24 13:58:25,394] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,396] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,397] [INFO] DQC Reference Directory: /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference
[2024-01-24 13:58:26,693] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,694] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,694] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2023db4-e980-4a42-ab90-661dd5ec6a22/GCF_002847305.1_ASM284730v1_genomic.fna.gz | prodigal -d GCF_002847305.1_ASM284730v1_genomic.fna/cds.fna -a GCF_002847305.1_ASM284730v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:39,741] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:39,741] [INFO] Task started: HMMsearch
[2024-01-24 13:58:39,741] [INFO] Running command: hmmsearch --tblout GCF_002847305.1_ASM284730v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/reference_markers.hmm GCF_002847305.1_ASM284730v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:40,059] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:40,060] [INFO] Found 6/6 markers.
[2024-01-24 13:58:40,105] [INFO] Query marker FASTA was written to GCF_002847305.1_ASM284730v1_genomic.fna/markers.fasta
[2024-01-24 13:58:40,106] [INFO] Task started: Blastn
[2024-01-24 13:58:40,106] [INFO] Running command: blastn -query GCF_002847305.1_ASM284730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/reference_markers.fasta -out GCF_002847305.1_ASM284730v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:41,043] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:41,047] [INFO] Selected 18 target genomes.
[2024-01-24 13:58:41,047] [INFO] Target genome list was writen to GCF_002847305.1_ASM284730v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:41,066] [INFO] Task started: fastANI
[2024-01-24 13:58:41,066] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2023db4-e980-4a42-ab90-661dd5ec6a22/GCF_002847305.1_ASM284730v1_genomic.fna.gz --refList GCF_002847305.1_ASM284730v1_genomic.fna/target_genomes.txt --output GCF_002847305.1_ASM284730v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:56,082] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:56,082] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:56,083] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:56,098] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:56,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:56,099] [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 tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	100.0	1313	1316	95	conclusive
Paracoccus zhejiangensis	strain=J6	GCA_002847445.1	1077935	1077935	type	True	81.4077	844	1316	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	79.8537	548	1316	95	below_threshold
Paracoccus lutimaris	strain=CECT 8525	GCA_003337565.1	1490030	1490030	type	True	79.846	551	1316	95	below_threshold
Paracoccus nototheniae	strain=I-41R45	GCA_004335005.1	2489002	2489002	type	True	79.7894	536	1316	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	79.7027	604	1316	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	79.6692	576	1316	95	below_threshold
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	79.5371	573	1316	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	79.4511	512	1316	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	79.4476	491	1316	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	79.3637	531	1316	95	below_threshold
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	79.3604	468	1316	95	below_threshold
Paracoccus gahaiensis	strain=KCTC 42687	GCA_005048225.1	1706839	1706839	type	True	79.3569	533	1316	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	79.3099	509	1316	95	below_threshold
Paracoccus sediminis	strain=DSM 26170	GCA_900188295.1	1214787	1214787	type	True	79.1826	481	1316	95	below_threshold
Paracoccus lichenicola	strain=YIM 132242	GCA_009708075.1	2665644	2665644	type	True	79.1198	491	1316	95	below_threshold
Paracoccus binzhouensis	strain=wg1	GCA_016446475.1	2796149	2796149	type	True	79.0552	515	1316	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.7313	424	1316	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:56,101] [INFO] DFAST Taxonomy check result was written to GCF_002847305.1_ASM284730v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:56,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:56,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:56,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/checkm_data
[2024-01-24 13:58:56,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:56,145] [INFO] Task started: CheckM
[2024-01-24 13:58:56,146] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002847305.1_ASM284730v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002847305.1_ASM284730v1_genomic.fna/checkm_input GCF_002847305.1_ASM284730v1_genomic.fna/checkm_result
[2024-01-24 13:59:35,473] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:35,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:35,491] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:35,491] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:35,492] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002847305.1_ASM284730v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:35,492] [INFO] Task started: Blastn
[2024-01-24 13:59:35,492] [INFO] Running command: blastn -query GCF_002847305.1_ASM284730v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg90b92d21-f621-4a91-94f3-d2759f5b0ceb/dqc_reference/reference_markers_gtdb.fasta -out GCF_002847305.1_ASM284730v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:36,967] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:36,970] [INFO] Selected 15 target genomes.
[2024-01-24 13:59:36,970] [INFO] Target genome list was writen to GCF_002847305.1_ASM284730v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:37,005] [INFO] Task started: fastANI
[2024-01-24 13:59:37,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2023db4-e980-4a42-ab90-661dd5ec6a22/GCF_002847305.1_ASM284730v1_genomic.fna.gz --refList GCF_002847305.1_ASM284730v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002847305.1_ASM284730v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:49,477] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:49,490] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:49,491] [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_002847305.1	s__Paracoccus sp002847305	100.0	1313	1316	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_007096355.1	s__Paracoccus sp007096355	82.1746	848	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002847445.1	s__Paracoccus zhejiangensis	81.4165	842	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860165.1	s__Paracoccus sp018860165	80.2959	627	1316	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	79.8732	544	1316	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	79.8449	552	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004335005.1	s__Paracoccus sp004335005	79.7663	539	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002294185.1	s__Paracoccus sp002294185	79.7209	546	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_003709565.1	s__Paracoccus siganidrum	79.7092	604	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_017744015.1	s__Paracoccus sp002732665	79.6337	559	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_900111675.1	s__Paracoccus homiensis	79.5612	572	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	79.3776	468	1316	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	79.3264	532	1316	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	79.1291	490	1316	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869875.1	s__Paracoccus sp016869875	78.805	333	1316	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 13:59:49,493] [INFO] GTDB search result was written to GCF_002847305.1_ASM284730v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:49,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:49,498] [INFO] DFAST_QC result json was written to GCF_002847305.1_ASM284730v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:49,498] [INFO] DFAST_QC completed!
[2024-01-24 13:59:49,498] [INFO] Total running time: 0h1m24s