[2024-01-24 10:57:19,770] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:19,772] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:19,772] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference
[2024-01-24 10:57:22,297] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:22,298] [INFO] Task started: Prodigal
[2024-01-24 10:57:22,299] [INFO] Running command: gunzip -c /var/lib/cwl/stg71e3979e-6da3-4d96-a6b7-715a1026f640/GCF_014640355.1_ASM1464035v1_genomic.fna.gz | prodigal -d GCF_014640355.1_ASM1464035v1_genomic.fna/cds.fna -a GCF_014640355.1_ASM1464035v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:37,484] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:37,485] [INFO] Task started: HMMsearch
[2024-01-24 10:57:37,485] [INFO] Running command: hmmsearch --tblout GCF_014640355.1_ASM1464035v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/reference_markers.hmm GCF_014640355.1_ASM1464035v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:37,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:37,778] [INFO] Found 6/6 markers.
[2024-01-24 10:57:37,823] [INFO] Query marker FASTA was written to GCF_014640355.1_ASM1464035v1_genomic.fna/markers.fasta
[2024-01-24 10:57:37,823] [INFO] Task started: Blastn
[2024-01-24 10:57:37,823] [INFO] Running command: blastn -query GCF_014640355.1_ASM1464035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/reference_markers.fasta -out GCF_014640355.1_ASM1464035v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:38,456] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:38,460] [INFO] Selected 15 target genomes.
[2024-01-24 10:57:38,461] [INFO] Target genome list was writen to GCF_014640355.1_ASM1464035v1_genomic.fna/target_genomes.txt
[2024-01-24 10:57:38,511] [INFO] Task started: fastANI
[2024-01-24 10:57:38,512] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e3979e-6da3-4d96-a6b7-715a1026f640/GCF_014640355.1_ASM1464035v1_genomic.fna.gz --refList GCF_014640355.1_ASM1464035v1_genomic.fna/target_genomes.txt --output GCF_014640355.1_ASM1464035v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:52,606] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:52,607] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:52,608] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:52,621] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:52,621] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:52,621] [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
Silvibacterium dinghuense	strain=CGMCC 1.13007	GCA_014640355.1	1560006	1560006	type	True	100.0	1700	1700	95	conclusive
Silvibacterium dinghuense	strain=DHOF10	GCA_004123295.1	1560006	1560006	type	True	99.9989	1699	1700	95	conclusive
Silvibacterium bohemicum	strain=S15	GCA_001006305.1	1577686	1577686	type	True	78.4103	565	1700	95	below_threshold
Silvibacterium bohemicum	strain=DSM 103733	GCA_014201455.1	1577686	1577686	type	True	78.3778	561	1700	95	below_threshold
Paracidobacterium acidisoli	strain=4G-K13	GCA_003428625.2	2303751	2303751	type	True	77.931	365	1700	95	below_threshold
Acidobacterium capsulatum	strain=ATCC 51196	GCA_000022565.1	33075	33075	type	True	77.7876	300	1700	95	below_threshold
Alloacidobacterium dinghuense	strain=4Y35	GCA_014274465.1	2763107	2763107	type	True	77.2579	228	1700	95	below_threshold
Granulicella rosea	strain=DSM 18704	GCA_900188085.1	474952	474952	type	True	77.253	262	1700	95	below_threshold
Granulicella mallensis	strain=MP5ACTX8	GCA_000178955.2	940614	940614	type	True	76.9413	231	1700	95	below_threshold
Granulicella pectinivorans	strain=DSM 21001	GCA_900114625.1	474950	474950	type	True	76.8309	194	1700	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	75.15	64	1700	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:52,623] [INFO] DFAST Taxonomy check result was written to GCF_014640355.1_ASM1464035v1_genomic.fna/tc_result.tsv
[2024-01-24 10:57:52,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:52,624] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:52,624] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/checkm_data
[2024-01-24 10:57:52,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:52,674] [INFO] Task started: CheckM
[2024-01-24 10:57:52,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014640355.1_ASM1464035v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014640355.1_ASM1464035v1_genomic.fna/checkm_input GCF_014640355.1_ASM1464035v1_genomic.fna/checkm_result
[2024-01-24 10:58:37,684] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:37,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:37,707] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:37,707] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:37,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014640355.1_ASM1464035v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:37,708] [INFO] Task started: Blastn
[2024-01-24 10:58:37,708] [INFO] Running command: blastn -query GCF_014640355.1_ASM1464035v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f484c08-1bc5-4a69-91dd-bdd176e7a073/dqc_reference/reference_markers_gtdb.fasta -out GCF_014640355.1_ASM1464035v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:38,679] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:38,683] [INFO] Selected 19 target genomes.
[2024-01-24 10:58:38,683] [INFO] Target genome list was writen to GCF_014640355.1_ASM1464035v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:38,715] [INFO] Task started: fastANI
[2024-01-24 10:58:38,715] [INFO] Running command: fastANI --query /var/lib/cwl/stg71e3979e-6da3-4d96-a6b7-715a1026f640/GCF_014640355.1_ASM1464035v1_genomic.fna.gz --refList GCF_014640355.1_ASM1464035v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014640355.1_ASM1464035v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:55,127] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:55,146] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:55,146] [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_004123295.1	s__Silvibacterium dinghuense	99.9989	1699	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001006305.1	s__Silvibacterium bohemicum	78.3834	569	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003428625.2	s__Palsa-343 sp003428625	77.9214	366	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Palsa-343	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000022565.1	s__Acidobacterium capsulatum	77.801	298	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_011333575.1	s__Acidobacterium capsulatum_A	77.7356	255	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013285705.1	s__Acidobacterium_A sp013285705	77.7126	156	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009765985.1	s__Acidobacterium_A sp009765985	77.3891	254	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014274465.1	s__Acidobacterium_A sp014274465	77.2579	228	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013289875.1	s__Silvibacterium sp013289875	77.2411	268	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188085.1	s__Granulicella_C rosea	77.1943	262	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019234945.1	s__Silvibacterium sp019234945	77.0336	207	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Silvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178955.2	s__Granulicella_A mallensis	76.9512	231	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114625.1	s__Granulicella_C pectinivorans	76.8329	194	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Granulicella_C	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015655315.1	s__Acidobacterium_A sp015655315	76.6081	194	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Acidobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009781125.1	s__Edaphobacter sp009781125	76.4654	101	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Edaphobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903828675.1	s__Terracidiphilus sp903828675	76.2211	150	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__Acidobacteriaceae;g__Terracidiphilus	95.0	99.87	99.75	0.95	0.93	4	-
GCA_019236695.1	s__JAFAIN01 sp019236695	75.7649	51	1700	d__Bacteria;p__Acidobacteriota;c__Acidobacteriae;o__Acidobacteriales;f__CAINCZ01;g__JAFAIN01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_904061905.1	s__Pseudomonas_E carbonaria	75.1601	63	1700	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:55,148] [INFO] GTDB search result was written to GCF_014640355.1_ASM1464035v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:55,148] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:55,152] [INFO] DFAST_QC result json was written to GCF_014640355.1_ASM1464035v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:55,152] [INFO] DFAST_QC completed!
[2024-01-24 10:58:55,152] [INFO] Total running time: 0h1m35s