[2024-01-24 13:01:26,505] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:26,508] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:26,508] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference
[2024-01-24 13:01:27,755] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:27,756] [INFO] Task started: Prodigal
[2024-01-24 13:01:27,756] [INFO] Running command: gunzip -c /var/lib/cwl/stg19993f0b-65d7-4bc5-a013-edc3d58bff8f/GCF_003034995.1_ASM303499v1_genomic.fna.gz | prodigal -d GCF_003034995.1_ASM303499v1_genomic.fna/cds.fna -a GCF_003034995.1_ASM303499v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:37,471] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:37,472] [INFO] Task started: HMMsearch
[2024-01-24 13:01:37,472] [INFO] Running command: hmmsearch --tblout GCF_003034995.1_ASM303499v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/reference_markers.hmm GCF_003034995.1_ASM303499v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:37,724] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:37,725] [INFO] Found 6/6 markers.
[2024-01-24 13:01:37,761] [INFO] Query marker FASTA was written to GCF_003034995.1_ASM303499v1_genomic.fna/markers.fasta
[2024-01-24 13:01:37,762] [INFO] Task started: Blastn
[2024-01-24 13:01:37,762] [INFO] Running command: blastn -query GCF_003034995.1_ASM303499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/reference_markers.fasta -out GCF_003034995.1_ASM303499v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:38,779] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:38,782] [INFO] Selected 17 target genomes.
[2024-01-24 13:01:38,783] [INFO] Target genome list was writen to GCF_003034995.1_ASM303499v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:38,815] [INFO] Task started: fastANI
[2024-01-24 13:01:38,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg19993f0b-65d7-4bc5-a013-edc3d58bff8f/GCF_003034995.1_ASM303499v1_genomic.fna.gz --refList GCF_003034995.1_ASM303499v1_genomic.fna/target_genomes.txt --output GCF_003034995.1_ASM303499v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:51,347] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:51,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:51,348] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:51,372] [INFO] Found 17 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:01:51,373] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:51,373] [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
Phaeovulum veldkampii	strain=DSM 11550	GCA_003034995.1	33049	33049	type	True	100.0	1016	1019	95	conclusive
Phaeovulum veldkampii	strain=DSM 11550	GCA_004363195.1	33049	33049	type	True	99.9973	1015	1019	95	conclusive
Phaeovulum veldkampii	strain=DSM 11550	GCA_016653435.1	33049	33049	type	True	99.9679	941	1019	95	conclusive
Phaeovulum vinaykumarii	strain=JA123	GCA_900217755.1	407234	407234	type	True	80.4109	586	1019	95	below_threshold
Phaeovulum vinaykumarii	strain=DSM 18714	GCA_900156695.1	407234	407234	type	True	80.4031	593	1019	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	79.6158	539	1019	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.612	507	1019	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009881095.1	1465486	1465486	type	True	79.3931	520	1019	95	below_threshold
Frigidibacter albus	strain=SP32	GCA_009908165.1	1465486	1465486	type	True	79.3588	520	1019	95	below_threshold
Paracoccus yeei	strain=G1212	GCA_002196965.1	147645	147645	type	True	78.9743	411	1019	95	below_threshold
Paracoccus yeei	strain=ATCC BAA-599	GCA_000622145.1	147645	147645	type	True	78.9284	426	1019	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.8758	442	1019	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.5606	376	1019	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	78.3199	421	1019	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	78.1732	364	1019	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	78.0788	319	1019	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	77.9897	334	1019	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:51,381] [INFO] DFAST Taxonomy check result was written to GCF_003034995.1_ASM303499v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:51,382] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:51,382] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:51,383] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/checkm_data
[2024-01-24 13:01:51,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:51,421] [INFO] Task started: CheckM
[2024-01-24 13:01:51,421] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003034995.1_ASM303499v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003034995.1_ASM303499v1_genomic.fna/checkm_input GCF_003034995.1_ASM303499v1_genomic.fna/checkm_result
[2024-01-24 13:02:25,163] [INFO] Task succeeded: CheckM
[2024-01-24 13:02:25,164] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:02:25,185] [INFO] ===== Completeness check finished =====
[2024-01-24 13:02:25,186] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:02:25,186] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003034995.1_ASM303499v1_genomic.fna/markers.fasta)
[2024-01-24 13:02:25,186] [INFO] Task started: Blastn
[2024-01-24 13:02:25,187] [INFO] Running command: blastn -query GCF_003034995.1_ASM303499v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a766908-18d8-40f7-82de-a5e4cd6f1985/dqc_reference/reference_markers_gtdb.fasta -out GCF_003034995.1_ASM303499v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:02:26,929] [INFO] Task succeeded: Blastn
[2024-01-24 13:02:26,933] [INFO] Selected 19 target genomes.
[2024-01-24 13:02:26,933] [INFO] Target genome list was writen to GCF_003034995.1_ASM303499v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:02:26,945] [INFO] Task started: fastANI
[2024-01-24 13:02:26,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg19993f0b-65d7-4bc5-a013-edc3d58bff8f/GCF_003034995.1_ASM303499v1_genomic.fna.gz --refList GCF_003034995.1_ASM303499v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003034995.1_ASM303499v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:02:40,780] [INFO] Task succeeded: fastANI
[2024-01-24 13:02:40,799] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:02:40,799] [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_003034995.1	s__Phaeovulum veldkampii	100.0	1016	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	99.98	99.97	0.97	0.94	3	conclusive
GCA_002452815.1	s__UBA6796 sp002452815	80.4161	538	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA6796	95.0	97.98	97.98	0.95	0.95	2	-
GCF_900156695.1	s__Bieblia_A vinaykumarii	80.3793	597	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Bieblia_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002422085.1	s__Phaeovulum sp002422085	80.0741	520	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763785.1	s__SZUA-611 sp014763785	79.9291	443	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842855.1	s__Phaeovulum sp002842855	79.7361	472	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	79.6069	540	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	79.5674	513	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002423245.1	s__Frigidibacter sp002423245	79.4837	460	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	98.55	98.55	0.85	0.85	2	-
GCF_009908165.1	s__Frigidibacter albus	79.3588	520	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	100.00	100.00	1.00	0.99	4	-
GCF_001447385.1	s__Paracoccus sp001447385	79.2592	456	1019	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	78.9238	426	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	96.0533	98.39	97.89	0.87	0.83	7	-
GCA_002841115.1	s__Albidovulum sp002841115	78.8403	429	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	78.7973	435	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_018139985.1	s__JAGSOU01 sp018139985	78.7671	429	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100045.1	s__Paracoccus denitrificans	78.7499	427	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.78	98.70	0.97	0.88	7	-
GCF_008271465.1	s__Tabrizicola flagellata	78.3548	417	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013415485.1	s__PUOA01 sp003567395	78.1622	365	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__PUOA01	95.0	98.54	98.26	0.95	0.89	5	-
GCA_016792685.1	s__Tabrizicola sp016792685	77.7351	267	1019	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:02:40,801] [INFO] GTDB search result was written to GCF_003034995.1_ASM303499v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:02:40,801] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:02:40,805] [INFO] DFAST_QC result json was written to GCF_003034995.1_ASM303499v1_genomic.fna/dqc_result.json
[2024-01-24 13:02:40,805] [INFO] DFAST_QC completed!
[2024-01-24 13:02:40,805] [INFO] Total running time: 0h1m14s