[2024-01-24 13:37:19,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:19,429] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:19,430] [INFO] DQC Reference Directory: /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference
[2024-01-24 13:37:20,766] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:20,767] [INFO] Task started: Prodigal
[2024-01-24 13:37:20,767] [INFO] Running command: gunzip -c /var/lib/cwl/stg2cfc356a-4ab0-454b-bf17-cd448f00280b/GCF_030295405.1_ASM3029540v1_genomic.fna.gz | prodigal -d GCF_030295405.1_ASM3029540v1_genomic.fna/cds.fna -a GCF_030295405.1_ASM3029540v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:36,076] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:36,077] [INFO] Task started: HMMsearch
[2024-01-24 13:37:36,077] [INFO] Running command: hmmsearch --tblout GCF_030295405.1_ASM3029540v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/reference_markers.hmm GCF_030295405.1_ASM3029540v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:36,392] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:36,394] [INFO] Found 6/6 markers.
[2024-01-24 13:37:36,455] [INFO] Query marker FASTA was written to GCF_030295405.1_ASM3029540v1_genomic.fna/markers.fasta
[2024-01-24 13:37:36,456] [INFO] Task started: Blastn
[2024-01-24 13:37:36,456] [INFO] Running command: blastn -query GCF_030295405.1_ASM3029540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/reference_markers.fasta -out GCF_030295405.1_ASM3029540v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:37,201] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:37,204] [INFO] Selected 23 target genomes.
[2024-01-24 13:37:37,205] [INFO] Target genome list was writen to GCF_030295405.1_ASM3029540v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:37,248] [INFO] Task started: fastANI
[2024-01-24 13:37:37,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cfc356a-4ab0-454b-bf17-cd448f00280b/GCF_030295405.1_ASM3029540v1_genomic.fna.gz --refList GCF_030295405.1_ASM3029540v1_genomic.fna/target_genomes.txt --output GCF_030295405.1_ASM3029540v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:53,926] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:53,926] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:53,927] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:53,942] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:53,942] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:53,943] [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
Geothrix fermentans	strain=DSM 14018	GCA_000428885.1	44676	44676	type	True	79.4722	547	1664	95	below_threshold
Holophaga foetida	strain=DSM 6591	GCA_000242615.3	35839	35839	type	True	78.7218	398	1664	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	75.8059	85	1664	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	75.654	152	1664	95	below_threshold
Desulfuromonas versatilis	strain=NIT-T3	GCA_019704135.1	2802975	2802975	type	True	75.6296	128	1664	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	75.5235	80	1664	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	75.4886	82	1664	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	75.4609	73	1664	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	75.4196	70	1664	95	below_threshold
Rubellimicrobium rubrum	strain=YIM 131921	GCA_006152115.1	2585369	2585369	type	True	75.3807	56	1664	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	75.3799	129	1664	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	75.198	52	1664	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	75.1762	122	1664	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	75.1181	157	1664	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.0998	230	1664	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	75.0527	117	1664	95	below_threshold
Caulobacter soli	strain=Ji-3-8	GCA_011045195.1	2708539	2708539	type	True	74.9416	127	1664	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:53,945] [INFO] DFAST Taxonomy check result was written to GCF_030295405.1_ASM3029540v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:53,945] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:53,945] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:53,945] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/checkm_data
[2024-01-24 13:37:53,947] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:54,002] [INFO] Task started: CheckM
[2024-01-24 13:37:54,002] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030295405.1_ASM3029540v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030295405.1_ASM3029540v1_genomic.fna/checkm_input GCF_030295405.1_ASM3029540v1_genomic.fna/checkm_result
[2024-01-24 13:38:49,854] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:49,856] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:49,877] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:49,878] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:49,878] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030295405.1_ASM3029540v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:49,878] [INFO] Task started: Blastn
[2024-01-24 13:38:49,879] [INFO] Running command: blastn -query GCF_030295405.1_ASM3029540v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9efba9b-51bd-4fce-80f4-f5f60fad7a35/dqc_reference/reference_markers_gtdb.fasta -out GCF_030295405.1_ASM3029540v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:50,905] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:50,909] [INFO] Selected 18 target genomes.
[2024-01-24 13:38:50,909] [INFO] Target genome list was writen to GCF_030295405.1_ASM3029540v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:50,947] [INFO] Task started: fastANI
[2024-01-24 13:38:50,947] [INFO] Running command: fastANI --query /var/lib/cwl/stg2cfc356a-4ab0-454b-bf17-cd448f00280b/GCF_030295405.1_ASM3029540v1_genomic.fna.gz --refList GCF_030295405.1_ASM3029540v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030295405.1_ASM3029540v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:39:04,498] [INFO] Task succeeded: fastANI
[2024-01-24 13:39:04,513] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:39:04,514] [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_002297665.1	s__Holophaga sp002297665	88.2557	962	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298155.1	s__Holophaga sp002298155	83.8319	752	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003165415.1	s__Holophaga sp003165415	80.9986	669	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428885.1	s__Geothrix fermentans	79.5211	542	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013390615.1	s__Geothrix sp013390615	79.3358	552	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903863195.1	s__Geothrix sp903863195	79.0089	505	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.63	99.47	0.91	0.90	5	-
GCA_002068835.1	s__Holophaga sp002068835	78.9882	373	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	98.95	98.95	0.82	0.82	2	-
GCF_000242615.2	s__Holophaga foetida	78.7358	396	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017859955.1	s__Holophaga sp017859955	78.7081	344	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903843705.1	s__Geothrix sp903843705	78.625	433	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Geothrix	95.0	99.09	98.86	0.88	0.85	6	-
GCA_016192145.1	s__JAFDVN01 sp016192145	78.2454	419	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__JAFDVN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016213735.1	s__JACQZU01 sp016213735	78.2419	456	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__JACQZU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002319925.1	s__Holophaga sp002319925	78.0121	313	1664	d__Bacteria;p__Acidobacteriota;c__Holophagae;o__Holophagales;f__Holophagaceae;g__Holophaga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:39:04,516] [INFO] GTDB search result was written to GCF_030295405.1_ASM3029540v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:39:04,516] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:39:04,523] [INFO] DFAST_QC result json was written to GCF_030295405.1_ASM3029540v1_genomic.fna/dqc_result.json
[2024-01-24 13:39:04,524] [INFO] DFAST_QC completed!
[2024-01-24 13:39:04,524] [INFO] Total running time: 0h1m45s