[2024-01-24 13:09:34,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,044] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,044] [INFO] DQC Reference Directory: /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference
[2024-01-24 13:09:35,392] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,393] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,393] [INFO] Running command: gunzip -c /var/lib/cwl/stgae8b7d2b-266f-4fb0-95bc-7125e8a31ae5/GCF_004135645.1_ASM413564v1_genomic.fna.gz | prodigal -d GCF_004135645.1_ASM413564v1_genomic.fna/cds.fna -a GCF_004135645.1_ASM413564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:45,176] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:45,177] [INFO] Task started: HMMsearch
[2024-01-24 13:09:45,177] [INFO] Running command: hmmsearch --tblout GCF_004135645.1_ASM413564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/reference_markers.hmm GCF_004135645.1_ASM413564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:45,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:45,395] [INFO] Found 6/6 markers.
[2024-01-24 13:09:45,432] [INFO] Query marker FASTA was written to GCF_004135645.1_ASM413564v1_genomic.fna/markers.fasta
[2024-01-24 13:09:45,433] [INFO] Task started: Blastn
[2024-01-24 13:09:45,433] [INFO] Running command: blastn -query GCF_004135645.1_ASM413564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/reference_markers.fasta -out GCF_004135645.1_ASM413564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:46,176] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:46,180] [INFO] Selected 17 target genomes.
[2024-01-24 13:09:46,180] [INFO] Target genome list was writen to GCF_004135645.1_ASM413564v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:46,188] [INFO] Task started: fastANI
[2024-01-24 13:09:46,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgae8b7d2b-266f-4fb0-95bc-7125e8a31ae5/GCF_004135645.1_ASM413564v1_genomic.fna.gz --refList GCF_004135645.1_ASM413564v1_genomic.fna/target_genomes.txt --output GCF_004135645.1_ASM413564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:55,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:55,285] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:55,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:55,296] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:09:55,296] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:55,296] [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
Senegalimassilia faecalis	strain=KGMB04484	GCA_004135645.1	2509433	2509433	type	True	100.0	909	915	95	conclusive
Senegalimassilia anaerobia	strain=type strain: JC110	GCA_000236865.1	1473216	1473216	type	True	85.0149	560	915	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	80.2126	371	915	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	79.869	358	915	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	79.7963	358	915	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003339815.1	242230	242230	type	True	79.7943	344	915	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	79.7685	346	915	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	79.7551	340	915	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	79.7263	340	915	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_014192995.1	572010	572010	type	True	79.36	189	915	95	below_threshold
Slackia isoflavoniconvertens	strain=DSM 22006	GCA_003725955.1	572010	572010	type	True	79.1193	180	915	95	below_threshold
Collinsella stercoris	strain=DSM 13279	GCA_025149625.1	147206	147206	type	True	78.9517	86	915	95	below_threshold
Slackia faecicanis	strain=DSM 17537	GCA_003725295.1	255723	255723	type	True	78.5099	191	915	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:55,298] [INFO] DFAST Taxonomy check result was written to GCF_004135645.1_ASM413564v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:55,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:55,299] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:55,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/checkm_data
[2024-01-24 13:09:55,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:55,329] [INFO] Task started: CheckM
[2024-01-24 13:09:55,329] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004135645.1_ASM413564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004135645.1_ASM413564v1_genomic.fna/checkm_input GCF_004135645.1_ASM413564v1_genomic.fna/checkm_result
[2024-01-24 13:10:26,098] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:26,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:26,117] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:26,117] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:26,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004135645.1_ASM413564v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:26,118] [INFO] Task started: Blastn
[2024-01-24 13:10:26,118] [INFO] Running command: blastn -query GCF_004135645.1_ASM413564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg68a012ad-0822-4cfd-b828-203427ac96b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_004135645.1_ASM413564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:27,341] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:27,345] [INFO] Selected 12 target genomes.
[2024-01-24 13:10:27,345] [INFO] Target genome list was writen to GCF_004135645.1_ASM413564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:27,353] [INFO] Task started: fastANI
[2024-01-24 13:10:27,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgae8b7d2b-266f-4fb0-95bc-7125e8a31ae5/GCF_004135645.1_ASM413564v1_genomic.fna.gz --refList GCF_004135645.1_ASM413564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004135645.1_ASM413564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:34,048] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:34,059] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:34,059] [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_004135645.1	s__Senegalimassilia faecalis	100.0	908	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.85	96.73	0.92	0.89	4	conclusive
GCA_905215325.1	s__Senegalimassilia sp905215325	85.0969	489	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000236865.1	s__Senegalimassilia anaerobia	85.0003	561	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	96.57	95.07	0.88	0.81	7	-
GCA_900550055.1	s__Senegalimassilia sp900550055	84.4169	437	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	97.04	96.58	0.76	0.72	3	-
GCA_002431805.1	s__Senegalimassilia sp002431805	83.7106	458	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Senegalimassilia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834925.2	s__Eggerthella sp014287365	80.2107	369	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_000024265.1	s__Eggerthella lenta	79.8773	357	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	98.39	97.51	0.89	0.82	72	-
GCF_003339815.1	s__Eggerthella sinensis	79.8	344	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	99.07	98.15	0.94	0.88	3	-
GCF_002159915.1	s__Rubneribacter sp002159915	79.3454	289	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Rubneribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003725955.1	s__Slackia_A isoflavoniconvertens	79.0987	180	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Slackia_A	95.0	96.92	96.02	0.86	0.81	13	-
GCA_900552365.1	s__UMGS1502 sp900552365	78.4983	133	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UMGS1502	95.0	99.96	99.96	0.96	0.96	2	-
GCA_900557505.1	s__Collinsella sp900557505	78.2353	56	915	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Coriobacteriaceae;g__Collinsella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:34,061] [INFO] GTDB search result was written to GCF_004135645.1_ASM413564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:34,061] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:34,065] [INFO] DFAST_QC result json was written to GCF_004135645.1_ASM413564v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:34,065] [INFO] DFAST_QC completed!
[2024-01-24 13:10:34,065] [INFO] Total running time: 0h1m0s