[2024-01-25 18:00:20,633] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:20,634] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:20,634] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference
[2024-01-25 18:00:21,798] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:21,799] [INFO] Task started: Prodigal
[2024-01-25 18:00:21,799] [INFO] Running command: gunzip -c /var/lib/cwl/stg662c17dd-0ed5-4ad6-81d4-d6ca30dada1f/GCF_025152575.1_ASM2515257v1_genomic.fna.gz | prodigal -d GCF_025152575.1_ASM2515257v1_genomic.fna/cds.fna -a GCF_025152575.1_ASM2515257v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:30,603] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:30,603] [INFO] Task started: HMMsearch
[2024-01-25 18:00:30,604] [INFO] Running command: hmmsearch --tblout GCF_025152575.1_ASM2515257v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/reference_markers.hmm GCF_025152575.1_ASM2515257v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:30,837] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:30,838] [INFO] Found 6/6 markers.
[2024-01-25 18:00:30,864] [INFO] Query marker FASTA was written to GCF_025152575.1_ASM2515257v1_genomic.fna/markers.fasta
[2024-01-25 18:00:30,864] [INFO] Task started: Blastn
[2024-01-25 18:00:30,864] [INFO] Running command: blastn -query GCF_025152575.1_ASM2515257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/reference_markers.fasta -out GCF_025152575.1_ASM2515257v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:31,451] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:31,454] [INFO] Selected 10 target genomes.
[2024-01-25 18:00:31,454] [INFO] Target genome list was writen to GCF_025152575.1_ASM2515257v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:31,467] [INFO] Task started: fastANI
[2024-01-25 18:00:31,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg662c17dd-0ed5-4ad6-81d4-d6ca30dada1f/GCF_025152575.1_ASM2515257v1_genomic.fna.gz --refList GCF_025152575.1_ASM2515257v1_genomic.fna/target_genomes.txt --output GCF_025152575.1_ASM2515257v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:00:37,459] [INFO] Task succeeded: fastANI
[2024-01-25 18:00:37,460] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:00:37,460] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:00:37,466] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:00:37,466] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:00:37,466] [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
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	100.0	1080	1081	95	conclusive
Subdoligranulum variabile	strain=DSM 15176	GCA_000157955.1	214851	214851	type	True	99.9537	1070	1081	95	conclusive
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	80.721	236	1081	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	80.4685	232	1081	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	79.7297	244	1081	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	79.5614	255	1081	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	78.9007	211	1081	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	78.8006	207	1081	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:00:37,468] [INFO] DFAST Taxonomy check result was written to GCF_025152575.1_ASM2515257v1_genomic.fna/tc_result.tsv
[2024-01-25 18:00:37,468] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:00:37,468] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:00:37,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/checkm_data
[2024-01-25 18:00:37,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:00:37,502] [INFO] Task started: CheckM
[2024-01-25 18:00:37,502] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025152575.1_ASM2515257v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025152575.1_ASM2515257v1_genomic.fna/checkm_input GCF_025152575.1_ASM2515257v1_genomic.fna/checkm_result
[2024-01-25 18:01:07,345] [INFO] Task succeeded: CheckM
[2024-01-25 18:01:07,347] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:01:07,368] [INFO] ===== Completeness check finished =====
[2024-01-25 18:01:07,368] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:01:07,368] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025152575.1_ASM2515257v1_genomic.fna/markers.fasta)
[2024-01-25 18:01:07,368] [INFO] Task started: Blastn
[2024-01-25 18:01:07,368] [INFO] Running command: blastn -query GCF_025152575.1_ASM2515257v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c2a83cd-23c8-434f-9f79-79f8af937269/dqc_reference/reference_markers_gtdb.fasta -out GCF_025152575.1_ASM2515257v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:01:08,316] [INFO] Task succeeded: Blastn
[2024-01-25 18:01:08,319] [INFO] Selected 10 target genomes.
[2024-01-25 18:01:08,319] [INFO] Target genome list was writen to GCF_025152575.1_ASM2515257v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:01:08,328] [INFO] Task started: fastANI
[2024-01-25 18:01:08,328] [INFO] Running command: fastANI --query /var/lib/cwl/stg662c17dd-0ed5-4ad6-81d4-d6ca30dada1f/GCF_025152575.1_ASM2515257v1_genomic.fna.gz --refList GCF_025152575.1_ASM2515257v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025152575.1_ASM2515257v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:01:15,197] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:15,204] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:01:15,204] [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_000157955.1	s__Gemmiger variabilis	99.9537	1070	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_900545545.1	s__Gemmiger sp900545545	86.3819	628	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	96.26	96.20	0.77	0.76	3	-
GCA_019116445.1	s__Gemmiger excrementigallinarum	86.1467	580	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904374465.1	s__Gemmiger sp904374465	85.434	570	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116705.1	s__Gemmiger avistercoris	83.2645	406	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	99.94	99.94	0.92	0.92	2	-
GCA_019116485.1	s__Gemmiger excrementavium	83.143	497	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003343905.1	s__Gemmiger variabilis_C	82.4611	497	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016900095.1	s__Gemmiger formicilis_A	82.3684	459	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019115045.1	s__Gemmiger excrementipullorum	81.8356	427	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905214345.1	s__Gemmiger sp905214345	81.0495	406	1081	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Gemmiger	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:01:15,206] [INFO] GTDB search result was written to GCF_025152575.1_ASM2515257v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:01:15,207] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:01:15,211] [INFO] DFAST_QC result json was written to GCF_025152575.1_ASM2515257v1_genomic.fna/dqc_result.json
[2024-01-25 18:01:15,212] [INFO] DFAST_QC completed!
[2024-01-25 18:01:15,212] [INFO] Total running time: 0h0m55s