[2023-06-29 19:13:37,967] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:13:37,970] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:13:37,970] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference
[2023-06-29 19:13:41,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:13:41,501] [INFO] Task started: Prodigal
[2023-06-29 19:13:41,501] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ba59c75-332f-4d2d-830a-91b4dc180361/GCA_021621235.1_ASM2162123v1_genomic.fna.gz | prodigal -d GCA_021621235.1_ASM2162123v1_genomic.fna/cds.fna -a GCA_021621235.1_ASM2162123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:13:48,569] [INFO] Task succeeded: Prodigal
[2023-06-29 19:13:48,570] [INFO] Task started: HMMsearch
[2023-06-29 19:13:48,570] [INFO] Running command: hmmsearch --tblout GCA_021621235.1_ASM2162123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/reference_markers.hmm GCA_021621235.1_ASM2162123v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:13:48,847] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:13:48,848] [INFO] Found 6/6 markers.
[2023-06-29 19:13:48,875] [INFO] Query marker FASTA was written to GCA_021621235.1_ASM2162123v1_genomic.fna/markers.fasta
[2023-06-29 19:13:48,875] [INFO] Task started: Blastn
[2023-06-29 19:13:48,876] [INFO] Running command: blastn -query GCA_021621235.1_ASM2162123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/reference_markers.fasta -out GCA_021621235.1_ASM2162123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:13:49,536] [INFO] Task succeeded: Blastn
[2023-06-29 19:13:49,541] [INFO] Selected 8 target genomes.
[2023-06-29 19:13:49,542] [INFO] Target genome list was writen to GCA_021621235.1_ASM2162123v1_genomic.fna/target_genomes.txt
[2023-06-29 19:13:49,545] [INFO] Task started: fastANI
[2023-06-29 19:13:49,545] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba59c75-332f-4d2d-830a-91b4dc180361/GCA_021621235.1_ASM2162123v1_genomic.fna.gz --refList GCA_021621235.1_ASM2162123v1_genomic.fna/target_genomes.txt --output GCA_021621235.1_ASM2162123v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:13:54,045] [INFO] Task succeeded: fastANI
[2023-06-29 19:13:54,046] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:13:54,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:13:54,057] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 19:13:54,058] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 19:13:54,058] [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
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	96.556	494	601	95	conclusive
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	85.2797	391	601	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	85.2301	397	601	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	85.2256	381	601	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	82.2506	54	601	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.1444	262	601	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	79.5144	135	601	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:13:54,060] [INFO] DFAST Taxonomy check result was written to GCA_021621235.1_ASM2162123v1_genomic.fna/tc_result.tsv
[2023-06-29 19:13:54,061] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:13:54,061] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:13:54,061] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/checkm_data
[2023-06-29 19:13:54,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:13:54,102] [INFO] Task started: CheckM
[2023-06-29 19:13:54,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021621235.1_ASM2162123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021621235.1_ASM2162123v1_genomic.fna/checkm_input GCA_021621235.1_ASM2162123v1_genomic.fna/checkm_result
[2023-06-29 19:14:21,289] [INFO] Task succeeded: CheckM
[2023-06-29 19:14:21,291] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 6.63%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 19:14:21,315] [INFO] ===== Completeness check finished =====
[2023-06-29 19:14:21,315] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:14:21,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021621235.1_ASM2162123v1_genomic.fna/markers.fasta)
[2023-06-29 19:14:21,316] [INFO] Task started: Blastn
[2023-06-29 19:14:21,317] [INFO] Running command: blastn -query GCA_021621235.1_ASM2162123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb77008d-be0c-49cd-828f-4972612061dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_021621235.1_ASM2162123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:14:22,245] [INFO] Task succeeded: Blastn
[2023-06-29 19:14:22,250] [INFO] Selected 10 target genomes.
[2023-06-29 19:14:22,251] [INFO] Target genome list was writen to GCA_021621235.1_ASM2162123v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:14:22,253] [INFO] Task started: fastANI
[2023-06-29 19:14:22,253] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ba59c75-332f-4d2d-830a-91b4dc180361/GCA_021621235.1_ASM2162123v1_genomic.fna.gz --refList GCA_021621235.1_ASM2162123v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021621235.1_ASM2162123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:14:27,499] [INFO] Task succeeded: fastANI
[2023-06-29 19:14:27,516] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:14:27,516] [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_003324185.1	s__Faecalibacterium prausnitzii	96.556	494	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	conclusive
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	94.5764	460	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCF_003287405.1	s__Faecalibacterium prausnitzii_J	94.2151	459	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	-
GCA_905215595.1	s__Faecalibacterium sp905215595	94.0503	326	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003449675.1	s__Faecalibacterium sp003449675	93.5641	317	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	96.56	96.55	0.80	0.74	3	-
GCA_900772565.1	s__Faecalibacterium sp900772565	93.3919	396	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900765705.1	s__Faecalibacterium sp900765705	91.1529	368	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.09	97.09	0.66	0.66	2	-
GCA_900539885.1	s__Faecalibacterium sp900539885	86.5764	364	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCA_900539945.1	s__Faecalibacterium sp900539945	86.2957	383	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCA_900765105.1	s__Faecalibacterium sp900765105	85.5256	300	601	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.27	98.27	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-29 19:14:27,518] [INFO] GTDB search result was written to GCA_021621235.1_ASM2162123v1_genomic.fna/result_gtdb.tsv
[2023-06-29 19:14:27,519] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:14:27,524] [INFO] DFAST_QC result json was written to GCA_021621235.1_ASM2162123v1_genomic.fna/dqc_result.json
[2023-06-29 19:14:27,524] [INFO] DFAST_QC completed!
[2023-06-29 19:14:27,524] [INFO] Total running time: 0h0m50s