[2024-01-24 13:27:55,245] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:55,247] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:55,247] [INFO] DQC Reference Directory: /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference
[2024-01-24 13:27:56,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:56,401] [INFO] Task started: Prodigal
[2024-01-24 13:27:56,401] [INFO] Running command: gunzip -c /var/lib/cwl/stg75434df1-606b-43da-90a6-0211ee31b943/GCF_000429765.1_ASM42976v1_genomic.fna.gz | prodigal -d GCF_000429765.1_ASM42976v1_genomic.fna/cds.fna -a GCF_000429765.1_ASM42976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:10,086] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:10,086] [INFO] Task started: HMMsearch
[2024-01-24 13:28:10,086] [INFO] Running command: hmmsearch --tblout GCF_000429765.1_ASM42976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/reference_markers.hmm GCF_000429765.1_ASM42976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:10,328] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:10,329] [INFO] Found 6/6 markers.
[2024-01-24 13:28:10,366] [INFO] Query marker FASTA was written to GCF_000429765.1_ASM42976v1_genomic.fna/markers.fasta
[2024-01-24 13:28:10,366] [INFO] Task started: Blastn
[2024-01-24 13:28:10,367] [INFO] Running command: blastn -query GCF_000429765.1_ASM42976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/reference_markers.fasta -out GCF_000429765.1_ASM42976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:11,487] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:11,491] [INFO] Selected 20 target genomes.
[2024-01-24 13:28:11,491] [INFO] Target genome list was writen to GCF_000429765.1_ASM42976v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:11,536] [INFO] Task started: fastANI
[2024-01-24 13:28:11,536] [INFO] Running command: fastANI --query /var/lib/cwl/stg75434df1-606b-43da-90a6-0211ee31b943/GCF_000429765.1_ASM42976v1_genomic.fna.gz --refList GCF_000429765.1_ASM42976v1_genomic.fna/target_genomes.txt --output GCF_000429765.1_ASM42976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:29,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:29,717] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:29,718] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:29,734] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:29,734] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:29,735] [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
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	100.0	1475	1476	95	conclusive
Gemmobacter megaterium	strain=CGMCC 1.11024	GCA_014636395.1	1086013	1086013	type	True	83.9874	924	1476	95	below_threshold
Gemmobacter megaterium	strain=DSM 26375	GCA_900156815.1	1086013	1086013	type	True	83.9443	934	1476	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	80.1385	552	1476	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.981	534	1476	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	79.5236	569	1476	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	79.3756	497	1476	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.2548	586	1476	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	79.245	511	1476	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	79.1667	509	1476	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	79.1377	533	1476	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	78.9503	463	1476	95	below_threshold
Pararhodobacter aggregans	strain=DSM 18938	GCA_003054005.1	404875	404875	type	True	78.7294	545	1476	95	below_threshold
Pararhodobacter aggregans	strain=D1-19	GCA_003075525.1	404875	404875	type	True	78.7241	558	1476	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.7194	454	1476	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.626	465	1476	95	below_threshold
Rhodovulum steppense	strain=DSM 21153	GCA_004339675.1	540251	540251	type	True	78.5541	470	1476	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	78.4781	466	1476	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	78.4593	434	1476	95	below_threshold
Pararhodobacter marinus	strain=CIC4N-9	GCA_003122215.1	2184063	2184063	type	True	78.4588	480	1476	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:29,736] [INFO] DFAST Taxonomy check result was written to GCF_000429765.1_ASM42976v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:29,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:29,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:29,737] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/checkm_data
[2024-01-24 13:28:29,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:29,783] [INFO] Task started: CheckM
[2024-01-24 13:28:29,783] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000429765.1_ASM42976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000429765.1_ASM42976v1_genomic.fna/checkm_input GCF_000429765.1_ASM42976v1_genomic.fna/checkm_result
[2024-01-24 13:29:27,181] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:27,182] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:27,198] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:27,199] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:27,199] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000429765.1_ASM42976v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:27,199] [INFO] Task started: Blastn
[2024-01-24 13:29:27,199] [INFO] Running command: blastn -query GCF_000429765.1_ASM42976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgae471013-fa43-44ae-b727-3204e0a73614/dqc_reference/reference_markers_gtdb.fasta -out GCF_000429765.1_ASM42976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:29,123] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:29,127] [INFO] Selected 21 target genomes.
[2024-01-24 13:29:29,127] [INFO] Target genome list was writen to GCF_000429765.1_ASM42976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:29,162] [INFO] Task started: fastANI
[2024-01-24 13:29:29,162] [INFO] Running command: fastANI --query /var/lib/cwl/stg75434df1-606b-43da-90a6-0211ee31b943/GCF_000429765.1_ASM42976v1_genomic.fna.gz --refList GCF_000429765.1_ASM42976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000429765.1_ASM42976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:46,650] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:46,666] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:46,666] [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_000429765.1	s__Wagnerdoeblera nectariphila	100.0	1475	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900156815.1	s__Wagnerdoeblera megaterium	83.9673	932	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014859945.1	s__UBA1943 sp014859945	79.8025	448	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA1943	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016446475.1	s__Paracoccus binzhouensis	79.6649	505	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	79.5055	572	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	79.2713	584	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.2607	562	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652355.1	s__Gemmobacter lanyuensis	79.1936	516	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	79.1386	536	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__KMS-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000763885.1	s__Paracoccus versutus	79.1181	516	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	98.67	98.17	0.87	0.76	7	-
GCA_000500915.1	s__Gemmobacter_B sp000500915	78.8774	442	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009380135.2	s__Fertoeibacter niger	78.8386	565	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518925.1	s__Paracoccus sp000518925	78.7687	499	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.13	98.71	0.90	0.89	3	-
GCF_003863335.1	s__Wagnerdoeblera faecalis	78.7403	494	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075525.1	s__Pararhodobacter aggregans	78.7214	559	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004339675.1	s__Rhodovulum steppense	78.5765	468	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	78.5469	436	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004054105.1	s__Wagnerdoeblera intermedia	78.393	466	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wagnerdoeblera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015654855.1	s__JAATGA01 sp015654855	78.3729	313	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAATGA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003060865.1	s__Gemmobacter_B sp003060865	78.247	449	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003990445.1	s__Pararhodobacter zhoushanensis	78.1744	456	1476	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:46,668] [INFO] GTDB search result was written to GCF_000429765.1_ASM42976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:46,669] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:46,673] [INFO] DFAST_QC result json was written to GCF_000429765.1_ASM42976v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:46,673] [INFO] DFAST_QC completed!
[2024-01-24 13:29:46,673] [INFO] Total running time: 0h1m51s