[2024-01-25 17:55:05,712] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:55:05,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:55:05,714] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference
[2024-01-25 17:55:06,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:55:06,864] [INFO] Task started: Prodigal
[2024-01-25 17:55:06,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg6dbf6bc3-c935-427b-a156-e3739e5bdcdb/GCF_016765775.1_ASM1676577v1_genomic.fna.gz | prodigal -d GCF_016765775.1_ASM1676577v1_genomic.fna/cds.fna -a GCF_016765775.1_ASM1676577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:55:18,302] [INFO] Task succeeded: Prodigal
[2024-01-25 17:55:18,302] [INFO] Task started: HMMsearch
[2024-01-25 17:55:18,302] [INFO] Running command: hmmsearch --tblout GCF_016765775.1_ASM1676577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/reference_markers.hmm GCF_016765775.1_ASM1676577v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:55:18,534] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:55:18,535] [INFO] Found 6/6 markers.
[2024-01-25 17:55:18,570] [INFO] Query marker FASTA was written to GCF_016765775.1_ASM1676577v1_genomic.fna/markers.fasta
[2024-01-25 17:55:18,571] [INFO] Task started: Blastn
[2024-01-25 17:55:18,571] [INFO] Running command: blastn -query GCF_016765775.1_ASM1676577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/reference_markers.fasta -out GCF_016765775.1_ASM1676577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:55:19,492] [INFO] Task succeeded: Blastn
[2024-01-25 17:55:19,494] [INFO] Selected 23 target genomes.
[2024-01-25 17:55:19,495] [INFO] Target genome list was writen to GCF_016765775.1_ASM1676577v1_genomic.fna/target_genomes.txt
[2024-01-25 17:55:19,509] [INFO] Task started: fastANI
[2024-01-25 17:55:19,509] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dbf6bc3-c935-427b-a156-e3739e5bdcdb/GCF_016765775.1_ASM1676577v1_genomic.fna.gz --refList GCF_016765775.1_ASM1676577v1_genomic.fna/target_genomes.txt --output GCF_016765775.1_ASM1676577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:55:39,044] [INFO] Task succeeded: fastANI
[2024-01-25 17:55:39,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:55:39,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:55:39,057] [INFO] Found 23 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:55:39,058] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:55:39,058] [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 caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	79.7114	628	1383	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	79.6146	607	1383	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	79.5363	610	1383	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	79.3921	584	1383	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	79.3601	590	1383	95	below_threshold
Gemmobacter lutimaris	strain=YJ-T1-11	GCA_003570715.1	2306023	2306023	type	True	79.3113	608	1383	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.2254	493	1383	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	79.0072	531	1383	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.9534	525	1383	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	78.9494	534	1383	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	78.9457	535	1383	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	78.9058	566	1383	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.9017	566	1383	95	below_threshold
Cereibacter changlensis	strain=DSM 18774	GCA_003254335.1	402884	402884	type	True	78.8598	542	1383	95	below_threshold
Cereibacter changlensis	strain=JA139	GCA_003034985.1	402884	402884	type	True	78.8593	526	1383	95	below_threshold
Gemmobacter nectariphilus	strain=DSM 15620	GCA_000429765.1	220343	220343	type	True	78.7378	502	1383	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	78.6503	496	1383	95	below_threshold
Gemmobacter aquarius	strain=HYN0069	GCA_003060865.1	2169400	2169400	type	True	78.6055	459	1383	95	below_threshold
Allgaiera indica	strain=CGMCC 1.10859	GCA_014653075.1	765699	765699	type	True	78.1503	439	1383	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_000763885.1	34007	34007	type	True	78.0846	457	1383	95	below_threshold
Paracoccus versutus	strain=DSM 582	GCA_003387045.1	34007	34007	type	True	78.0799	473	1383	95	below_threshold
Roseicitreum antarcticum	strain=ZS2-28	GCA_014681765.1	564137	564137	type	True	77.909	351	1383	95	below_threshold
Pseudorhodobacter aquimaris	strain=KCTC 23043	GCA_001202025.1	687412	687412	type	True	77.8832	369	1383	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:55:39,059] [INFO] DFAST Taxonomy check result was written to GCF_016765775.1_ASM1676577v1_genomic.fna/tc_result.tsv
[2024-01-25 17:55:39,061] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:55:39,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:55:39,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/checkm_data
[2024-01-25 17:55:39,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:55:39,104] [INFO] Task started: CheckM
[2024-01-25 17:55:39,105] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016765775.1_ASM1676577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016765775.1_ASM1676577v1_genomic.fna/checkm_input GCF_016765775.1_ASM1676577v1_genomic.fna/checkm_result
[2024-01-25 17:56:24,929] [INFO] Task succeeded: CheckM
[2024-01-25 17:56:24,930] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:56:24,951] [INFO] ===== Completeness check finished =====
[2024-01-25 17:56:24,951] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:56:24,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016765775.1_ASM1676577v1_genomic.fna/markers.fasta)
[2024-01-25 17:56:24,953] [INFO] Task started: Blastn
[2024-01-25 17:56:24,953] [INFO] Running command: blastn -query GCF_016765775.1_ASM1676577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d95521f-5ca3-4523-9d5a-63e728f1b14a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016765775.1_ASM1676577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:56:26,741] [INFO] Task succeeded: Blastn
[2024-01-25 17:56:26,745] [INFO] Selected 24 target genomes.
[2024-01-25 17:56:26,745] [INFO] Target genome list was writen to GCF_016765775.1_ASM1676577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:56:26,787] [INFO] Task started: fastANI
[2024-01-25 17:56:26,787] [INFO] Running command: fastANI --query /var/lib/cwl/stg6dbf6bc3-c935-427b-a156-e3739e5bdcdb/GCF_016765775.1_ASM1676577v1_genomic.fna.gz --refList GCF_016765775.1_ASM1676577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016765775.1_ASM1676577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:56:47,350] [INFO] Task succeeded: fastANI
[2024-01-25 17:56:47,364] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:56:47,364] [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_016765775.1	s__Pseudorhodobacter sp016765775	100.0	1379	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008271655.1	s__Gemmobacter caeruleus	79.6799	632	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110025.1	s__Gemmobacter aquatilis	79.627	606	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018798885.1	s__Gemmobacter sp018798885	79.5574	608	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009380135.2	s__Fertoeibacter niger	79.5388	621	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Fertoeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799285.1	s__Gemmobacter_D aestuarii	79.4506	568	1383	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_003054195.1	s__Gemmobacter caeni	79.4018	585	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	98.77	98.23	0.88	0.79	5	-
GCF_003570715.1	s__Gemmobacter lutimaris	79.3508	601	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900207575.1	s__Cereibacter_A ovatus	79.2402	491	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011059185.1	s__Gemmobacter_B sp011059185	79.2237	568	1383	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_002855575.1	s__Gemmobacter_B sp002855575	79.0557	546	1383	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_010915705.1	s__ETT8 sp010915705	79.0336	528	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002900965.1	s__ETT8 sp002900965	79.0194	546	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009908265.2	s__Gemmobacter_B sp009908265	78.9447	536	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003443995.1	s__ETT8 sp003443995	78.8864	568	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003034985.1	s__Cereibacter changlensis	78.8508	527	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cereibacter	95.0	98.07	96.18	0.89	0.78	3	-
GCF_003991405.1	s__Pseudorhodobacter sp003991405	78.8188	607	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176015.1	s__Pseudorhodobacter_B sp000176015	78.7637	503	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudorhodobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011008935.1	s__KMS-5 sp011008935	78.6627	502	1383	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_003060865.1	s__Gemmobacter_B sp003060865	78.6055	459	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Gemmobacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704435.1	s__JAAKGP01 sp016704435	78.5328	521	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAAKGP01	95.0	99.06	99.06	0.93	0.93	2	-
GCA_001828855.1	s__Cypionkella sp001828855	78.3866	497	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cypionkella	95.0	99.95	99.91	0.99	0.97	3	-
GCF_002900975.1	s__Tabrizicola aquatica	78.3737	455	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405985.1	s__Pseudogemmobacter sp016405985	78.3392	458	1383	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:56:47,365] [INFO] GTDB search result was written to GCF_016765775.1_ASM1676577v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:56:47,365] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:56:47,371] [INFO] DFAST_QC result json was written to GCF_016765775.1_ASM1676577v1_genomic.fna/dqc_result.json
[2024-01-25 17:56:47,371] [INFO] DFAST_QC completed!
[2024-01-25 17:56:47,371] [INFO] Total running time: 0h1m42s