[2024-01-24 11:43:39,618] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:39,621] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:39,621] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference
[2024-01-24 11:43:40,861] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:40,862] [INFO] Task started: Prodigal
[2024-01-24 11:43:40,862] [INFO] Running command: gunzip -c /var/lib/cwl/stg50d9cda2-f1d1-4aae-bb78-b1d694b5f9f2/GCF_013155295.1_ASM1315529v1_genomic.fna.gz | prodigal -d GCF_013155295.1_ASM1315529v1_genomic.fna/cds.fna -a GCF_013155295.1_ASM1315529v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:43:54,514] [INFO] Task succeeded: Prodigal
[2024-01-24 11:43:54,514] [INFO] Task started: HMMsearch
[2024-01-24 11:43:54,514] [INFO] Running command: hmmsearch --tblout GCF_013155295.1_ASM1315529v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/reference_markers.hmm GCF_013155295.1_ASM1315529v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:43:54,862] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:43:54,863] [INFO] Found 6/6 markers.
[2024-01-24 11:43:54,912] [INFO] Query marker FASTA was written to GCF_013155295.1_ASM1315529v1_genomic.fna/markers.fasta
[2024-01-24 11:43:54,913] [INFO] Task started: Blastn
[2024-01-24 11:43:54,913] [INFO] Running command: blastn -query GCF_013155295.1_ASM1315529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/reference_markers.fasta -out GCF_013155295.1_ASM1315529v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:43:55,986] [INFO] Task succeeded: Blastn
[2024-01-24 11:43:55,989] [INFO] Selected 19 target genomes.
[2024-01-24 11:43:55,990] [INFO] Target genome list was writen to GCF_013155295.1_ASM1315529v1_genomic.fna/target_genomes.txt
[2024-01-24 11:43:56,003] [INFO] Task started: fastANI
[2024-01-24 11:43:56,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d9cda2-f1d1-4aae-bb78-b1d694b5f9f2/GCF_013155295.1_ASM1315529v1_genomic.fna.gz --refList GCF_013155295.1_ASM1315529v1_genomic.fna/target_genomes.txt --output GCF_013155295.1_ASM1315529v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:12,415] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:12,416] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:12,416] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:12,432] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:12,432] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:12,432] [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
Pseudogemmobacter hezensis	strain=D13-10-4-6	GCA_013155295.1	2737662	2737662	type	True	100.0	1501	1506	95	conclusive
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	83.5767	972	1506	95	below_threshold
Gemmobacter serpentinus	strain=HB-1	GCA_008973825.1	2652247	2652247	type	True	78.8629	508	1506	95	below_threshold
Gemmobacter caeruleus	strain=N8	GCA_008271655.1	2595004	2595004	type	True	78.5598	510	1506	95	below_threshold
Gemmobacter caeni	strain=DSM 21823	GCA_003054195.1	589035	589035	type	True	78.5306	458	1506	95	below_threshold
Gemmobacter aquatilis	strain=DSM 3857	GCA_900110025.1	933059	933059	type	True	78.4904	478	1506	95	below_threshold
Gemmobacter caeni	strain=CGMCC 1.7745	GCA_007830625.1	589035	589035	type	True	78.4807	461	1506	95	below_threshold
Gemmobacter lanyuensis	strain=KCTC 23714	GCA_014652355.1	1054497	1054497	type	True	78.3918	431	1506	95	below_threshold
Gemmobacter fulva	strain=con5	GCA_018798885.1	2840474	2840474	type	True	78.3906	504	1506	95	below_threshold
Tabrizicola algicola	strain=ETT8	GCA_010915705.1	2709381	2709381	type	True	78.164	377	1506	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	78.1172	409	1506	95	below_threshold
Tabrizicola alkalilacus	strain=DJC	GCA_003443995.1	2305252	2305252	type	True	78.1141	449	1506	95	below_threshold
Rhodobacter flagellatus	strain=SYSU G03088	GCA_008271465.1	2593021	2593021	type	True	77.999	391	1506	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	77.9403	389	1506	95	below_threshold
Tabrizicola sediminis	strain=DRYC-M-16	GCA_004745575.1	2486418	2486418	type	True	77.9051	376	1506	95	below_threshold
Rhodobacter tardus	strain=CYK-10	GCA_009925085.1	2699202	2699202	type	True	77.8776	403	1506	95	below_threshold
Gemmobacter straminiformis	strain=CAM-8	GCA_014243445.1	2045119	2045119	type	True	77.8464	387	1506	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	77.6929	355	1506	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	77.5234	342	1506	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:12,434] [INFO] DFAST Taxonomy check result was written to GCF_013155295.1_ASM1315529v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:12,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:12,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:12,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/checkm_data
[2024-01-24 11:44:12,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:12,485] [INFO] Task started: CheckM
[2024-01-24 11:44:12,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013155295.1_ASM1315529v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013155295.1_ASM1315529v1_genomic.fna/checkm_input GCF_013155295.1_ASM1315529v1_genomic.fna/checkm_result
[2024-01-24 11:44:56,113] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:56,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:56,138] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:56,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:56,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013155295.1_ASM1315529v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:56,139] [INFO] Task started: Blastn
[2024-01-24 11:44:56,140] [INFO] Running command: blastn -query GCF_013155295.1_ASM1315529v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdef8661-3415-4c2a-a2fa-8c7be6666e39/dqc_reference/reference_markers_gtdb.fasta -out GCF_013155295.1_ASM1315529v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:57,825] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:57,828] [INFO] Selected 6 target genomes.
[2024-01-24 11:44:57,829] [INFO] Target genome list was writen to GCF_013155295.1_ASM1315529v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:57,834] [INFO] Task started: fastANI
[2024-01-24 11:44:57,834] [INFO] Running command: fastANI --query /var/lib/cwl/stg50d9cda2-f1d1-4aae-bb78-b1d694b5f9f2/GCF_013155295.1_ASM1315529v1_genomic.fna.gz --refList GCF_013155295.1_ASM1315529v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013155295.1_ASM1315529v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:04,318] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:04,331] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:04,331] [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_013155295.1	s__Pseudogemmobacter sp013155295	100.0	1501	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003290025.1	s__Pseudogemmobacter bohemicus	83.584	970	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016405985.1	s__Pseudogemmobacter sp016405985	83.2768	935	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105075.1	s__Pseudogemmobacter sp900105075	83.2015	920	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900609055.1	s__Pseudogemmobacter humi	81.0018	750	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudogemmobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010915705.1	s__ETT8 sp010915705	78.1482	378	1506	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__ETT8	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:04,333] [INFO] GTDB search result was written to GCF_013155295.1_ASM1315529v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:04,334] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:04,350] [INFO] DFAST_QC result json was written to GCF_013155295.1_ASM1315529v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:04,350] [INFO] DFAST_QC completed!
[2024-01-24 11:45:04,350] [INFO] Total running time: 0h1m25s