[2024-01-24 10:57:07,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:07,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:07,590] [INFO] DQC Reference Directory: /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference
[2024-01-24 10:57:08,802] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:08,803] [INFO] Task started: Prodigal
[2024-01-24 10:57:08,803] [INFO] Running command: gunzip -c /var/lib/cwl/stg591dfdef-dcee-4eaf-8dc7-01044684f5e5/GCF_025998535.1_ASM2599853v1_genomic.fna.gz | prodigal -d GCF_025998535.1_ASM2599853v1_genomic.fna/cds.fna -a GCF_025998535.1_ASM2599853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:19,503] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:19,504] [INFO] Task started: HMMsearch
[2024-01-24 10:57:19,504] [INFO] Running command: hmmsearch --tblout GCF_025998535.1_ASM2599853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/reference_markers.hmm GCF_025998535.1_ASM2599853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:19,806] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:19,808] [INFO] Found 6/6 markers.
[2024-01-24 10:57:19,843] [INFO] Query marker FASTA was written to GCF_025998535.1_ASM2599853v1_genomic.fna/markers.fasta
[2024-01-24 10:57:19,844] [INFO] Task started: Blastn
[2024-01-24 10:57:19,844] [INFO] Running command: blastn -query GCF_025998535.1_ASM2599853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/reference_markers.fasta -out GCF_025998535.1_ASM2599853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:20,505] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:20,509] [INFO] Selected 16 target genomes.
[2024-01-24 10:57:20,510] [INFO] Target genome list was writen to GCF_025998535.1_ASM2599853v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:20,518] [INFO] Task started: fastANI
[2024-01-24 10:57:20,518] [INFO] Running command: fastANI --query /var/lib/cwl/stg591dfdef-dcee-4eaf-8dc7-01044684f5e5/GCF_025998535.1_ASM2599853v1_genomic.fna.gz --refList GCF_025998535.1_ASM2599853v1_genomic.fna/target_genomes.txt --output GCF_025998535.1_ASM2599853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:30,652] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:30,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:30,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:30,664] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:57:30,665] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:57:30,665] [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
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.827	202	1198	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.3153	191	1198	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	77.2481	244	1198	95	below_threshold
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	76.8696	73	1198	95	below_threshold
Desulfobulbus rhabdoformis	strain=DSM 8777	GCA_016919065.1	34032	34032	type	True	76.6172	87	1198	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_016918515.1	1506996	1506996	type	True	76.3193	89	1198	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.279	91	1198	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	75.4827	52	1198	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:30,666] [INFO] DFAST Taxonomy check result was written to GCF_025998535.1_ASM2599853v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:30,667] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:30,667] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:30,667] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/checkm_data
[2024-01-24 10:57:30,669] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:30,709] [INFO] Task started: CheckM
[2024-01-24 10:57:30,709] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025998535.1_ASM2599853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025998535.1_ASM2599853v1_genomic.fna/checkm_input GCF_025998535.1_ASM2599853v1_genomic.fna/checkm_result
[2024-01-24 10:58:05,239] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:05,240] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:05,261] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:05,262] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:05,262] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025998535.1_ASM2599853v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:05,262] [INFO] Task started: Blastn
[2024-01-24 10:58:05,263] [INFO] Running command: blastn -query GCF_025998535.1_ASM2599853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg658a9f68-e65b-4638-922f-8edffc96b218/dqc_reference/reference_markers_gtdb.fasta -out GCF_025998535.1_ASM2599853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:06,281] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:06,291] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:06,291] [INFO] Target genome list was writen to GCF_025998535.1_ASM2599853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:06,374] [INFO] Task started: fastANI
[2024-01-24 10:58:06,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg591dfdef-dcee-4eaf-8dc7-01044684f5e5/GCF_025998535.1_ASM2599853v1_genomic.fna.gz --refList GCF_025998535.1_ASM2599853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025998535.1_ASM2599853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:17,920] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:17,939] [INFO] Found 19 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:58:17,940] [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
GCA_015484845.1	s__DRKI01 sp015484845	79.15	396	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051875.1	s__DRKI01 sp011051875	78.4746	326	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	99.14	99.09	0.93	0.90	3	-
GCF_000621145.1	s__Desulfobulbus elongatus	77.827	202	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003604995.1	s__UBA10518 sp003604995	77.668	158	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013151365.1	s__BMS3Abin13 sp013151365	77.3399	170	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__BMS3Abin13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015489765.1	s__DRLX01 sp015489765	77.3282	202	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017998195.1	s__Desulfobulbus sp017998195	77.3125	160	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	77.295	190	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429965.1	s__Desulfobulbus_A mediterraneus	77.2422	243	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051825.1	s__DRLX01 sp011051825	77.082	172	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRLX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782165.1	s__Desulfobulbus sp009782165	76.9888	86	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508005.1	s__UBA10518 sp003508005	76.9706	170	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__UBA10518	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842475.1	s__Desulfobulbus sp903842475	76.766	123	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019163135.1	s__Desulfobulbus sp019163135	76.7171	118	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778955.1	s__Desulfobulbus sp009778955	76.6783	113	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778235.1	s__Desulfobulbus sp009778235	76.651	115	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001873115.1	s__CG2-30-60-27 sp001873115	76.4618	87	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__CG2-30-60-27	95.0	99.49	99.49	0.83	0.83	2	-
GCA_001799285.1	s__UBA2262 sp001799285	76.2472	93	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744275.1	s__Desulfobulbus sp012744275	75.892	72	1198	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:17,941] [INFO] GTDB search result was written to GCF_025998535.1_ASM2599853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:17,942] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:17,946] [INFO] DFAST_QC result json was written to GCF_025998535.1_ASM2599853v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:17,946] [INFO] DFAST_QC completed!
[2024-01-24 10:58:17,946] [INFO] Total running time: 0h1m10s