[2023-06-29 14:51:01,755] [INFO] DFAST_QC pipeline started.
[2023-06-29 14:51:01,760] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 14:51:01,761] [INFO] DQC Reference Directory: /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference
[2023-06-29 14:51:03,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 14:51:03,135] [INFO] Task started: Prodigal
[2023-06-29 14:51:03,135] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ad7718e-7583-482a-a1d4-2d85dac38a16/GCA_021622795.1_ASM2162279v1_genomic.fna.gz | prodigal -d GCA_021622795.1_ASM2162279v1_genomic.fna/cds.fna -a GCA_021622795.1_ASM2162279v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 14:51:09,841] [INFO] Task succeeded: Prodigal
[2023-06-29 14:51:09,842] [INFO] Task started: HMMsearch
[2023-06-29 14:51:09,842] [INFO] Running command: hmmsearch --tblout GCA_021622795.1_ASM2162279v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/reference_markers.hmm GCA_021622795.1_ASM2162279v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 14:51:10,099] [INFO] Task succeeded: HMMsearch
[2023-06-29 14:51:10,101] [INFO] Found 6/6 markers.
[2023-06-29 14:51:10,127] [INFO] Query marker FASTA was written to GCA_021622795.1_ASM2162279v1_genomic.fna/markers.fasta
[2023-06-29 14:51:10,128] [INFO] Task started: Blastn
[2023-06-29 14:51:10,128] [INFO] Running command: blastn -query GCA_021622795.1_ASM2162279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/reference_markers.fasta -out GCA_021622795.1_ASM2162279v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:51:10,769] [INFO] Task succeeded: Blastn
[2023-06-29 14:51:10,772] [INFO] Selected 7 target genomes.
[2023-06-29 14:51:10,773] [INFO] Target genome list was writen to GCA_021622795.1_ASM2162279v1_genomic.fna/target_genomes.txt
[2023-06-29 14:51:10,774] [INFO] Task started: fastANI
[2023-06-29 14:51:10,774] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad7718e-7583-482a-a1d4-2d85dac38a16/GCA_021622795.1_ASM2162279v1_genomic.fna.gz --refList GCA_021622795.1_ASM2162279v1_genomic.fna/target_genomes.txt --output GCA_021622795.1_ASM2162279v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 14:51:14,585] [INFO] Task succeeded: fastANI
[2023-06-29 14:51:14,586] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 14:51:14,586] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 14:51:14,594] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 14:51:14,594] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 14:51:14,594] [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	94.1602	464	536	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.3549	378	536	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.309	384	536	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	83.9806	391	536	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	80.3846	254	536	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.4231	128	536	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.3163	133	536	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 14:51:14,597] [INFO] DFAST Taxonomy check result was written to GCA_021622795.1_ASM2162279v1_genomic.fna/tc_result.tsv
[2023-06-29 14:51:14,597] [INFO] ===== Taxonomy check completed =====
[2023-06-29 14:51:14,597] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 14:51:14,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/checkm_data
[2023-06-29 14:51:14,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 14:51:14,630] [INFO] Task started: CheckM
[2023-06-29 14:51:14,630] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021622795.1_ASM2162279v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021622795.1_ASM2162279v1_genomic.fna/checkm_input GCA_021622795.1_ASM2162279v1_genomic.fna/checkm_result
[2023-06-29 14:51:40,895] [INFO] Task succeeded: CheckM
[2023-06-29 14:51:40,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 6.25%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-29 14:51:40,917] [INFO] ===== Completeness check finished =====
[2023-06-29 14:51:40,918] [INFO] ===== Start GTDB Search =====
[2023-06-29 14:51:40,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021622795.1_ASM2162279v1_genomic.fna/markers.fasta)
[2023-06-29 14:51:40,919] [INFO] Task started: Blastn
[2023-06-29 14:51:40,919] [INFO] Running command: blastn -query GCA_021622795.1_ASM2162279v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06198243-91b2-4fca-8838-8b27f8ec3979/dqc_reference/reference_markers_gtdb.fasta -out GCA_021622795.1_ASM2162279v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 14:51:41,775] [INFO] Task succeeded: Blastn
[2023-06-29 14:51:41,780] [INFO] Selected 9 target genomes.
[2023-06-29 14:51:41,780] [INFO] Target genome list was writen to GCA_021622795.1_ASM2162279v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 14:51:41,781] [INFO] Task started: fastANI
[2023-06-29 14:51:41,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ad7718e-7583-482a-a1d4-2d85dac38a16/GCA_021622795.1_ASM2162279v1_genomic.fna.gz --refList GCA_021622795.1_ASM2162279v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021622795.1_ASM2162279v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 14:51:46,660] [INFO] Task succeeded: fastANI
[2023-06-29 14:51:46,668] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 14:51:46,669] [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_003287405.1	s__Faecalibacterium prausnitzii_J	97.2713	479	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.32	96.98	0.87	0.83	5	conclusive
GCA_900772565.1	s__Faecalibacterium sp900772565	94.2199	406	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	94.1973	463	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.64	96.12	0.86	0.79	47	-
GCF_002550015.1	s__Faecalibacterium prausnitzii_A	93.9748	446	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0612	96.42	95.34	0.88	0.83	7	-
GCA_905215595.1	s__Faecalibacterium sp905215595	93.1737	347	536	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	92.8622	330	536	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_900765705.1	s__Faecalibacterium sp900765705	91.1369	346	536	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_900539945.1	s__Faecalibacterium sp900539945	85.5563	379	536	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_900551435.1	s__Faecalibacterium sp900551435	82.4298	307	536	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.30	98.30	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-29 14:51:46,671] [INFO] GTDB search result was written to GCA_021622795.1_ASM2162279v1_genomic.fna/result_gtdb.tsv
[2023-06-29 14:51:46,672] [INFO] ===== GTDB Search completed =====
[2023-06-29 14:51:46,675] [INFO] DFAST_QC result json was written to GCA_021622795.1_ASM2162279v1_genomic.fna/dqc_result.json
[2023-06-29 14:51:46,675] [INFO] DFAST_QC completed!
[2023-06-29 14:51:46,675] [INFO] Total running time: 0h0m45s