[2023-06-28 16:01:14,390] [INFO] DFAST_QC pipeline started.
[2023-06-28 16:01:14,392] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 16:01:14,392] [INFO] DQC Reference Directory: /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference
[2023-06-28 16:01:15,573] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 16:01:15,574] [INFO] Task started: Prodigal
[2023-06-28 16:01:15,574] [INFO] Running command: gunzip -c /var/lib/cwl/stg83760053-c0bb-42e5-ad5a-da15b2f91f8a/GCA_019415205.1_ASM1941520v1_genomic.fna.gz | prodigal -d GCA_019415205.1_ASM1941520v1_genomic.fna/cds.fna -a GCA_019415205.1_ASM1941520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 16:01:23,152] [INFO] Task succeeded: Prodigal
[2023-06-28 16:01:23,152] [INFO] Task started: HMMsearch
[2023-06-28 16:01:23,153] [INFO] Running command: hmmsearch --tblout GCA_019415205.1_ASM1941520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/reference_markers.hmm GCA_019415205.1_ASM1941520v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 16:01:23,337] [INFO] Task succeeded: HMMsearch
[2023-06-28 16:01:23,339] [INFO] Found 6/6 markers.
[2023-06-28 16:01:23,364] [INFO] Query marker FASTA was written to GCA_019415205.1_ASM1941520v1_genomic.fna/markers.fasta
[2023-06-28 16:01:23,364] [INFO] Task started: Blastn
[2023-06-28 16:01:23,364] [INFO] Running command: blastn -query GCA_019415205.1_ASM1941520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/reference_markers.fasta -out GCA_019415205.1_ASM1941520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:24,067] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:24,071] [INFO] Selected 7 target genomes.
[2023-06-28 16:01:24,071] [INFO] Target genome list was writen to GCA_019415205.1_ASM1941520v1_genomic.fna/target_genomes.txt
[2023-06-28 16:01:24,072] [INFO] Task started: fastANI
[2023-06-28 16:01:24,072] [INFO] Running command: fastANI --query /var/lib/cwl/stg83760053-c0bb-42e5-ad5a-da15b2f91f8a/GCA_019415205.1_ASM1941520v1_genomic.fna.gz --refList GCA_019415205.1_ASM1941520v1_genomic.fna/target_genomes.txt --output GCA_019415205.1_ASM1941520v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 16:01:28,788] [INFO] Task succeeded: fastANI
[2023-06-28 16:01:28,788] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 16:01:28,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 16:01:28,795] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-28 16:01:28,795] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 16:01:28,795] [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 duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	96.8008	670	822	95	conclusive
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	96.7305	676	822	95	conclusive
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	85.834	576	822	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	84.8903	553	822	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.4304	380	822	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.6164	193	822	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 16:01:28,797] [INFO] DFAST Taxonomy check result was written to GCA_019415205.1_ASM1941520v1_genomic.fna/tc_result.tsv
[2023-06-28 16:01:28,798] [INFO] ===== Taxonomy check completed =====
[2023-06-28 16:01:28,798] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 16:01:28,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/checkm_data
[2023-06-28 16:01:28,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 16:01:28,827] [INFO] Task started: CheckM
[2023-06-28 16:01:28,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019415205.1_ASM1941520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019415205.1_ASM1941520v1_genomic.fna/checkm_input GCA_019415205.1_ASM1941520v1_genomic.fna/checkm_result
[2023-06-28 16:01:55,399] [INFO] Task succeeded: CheckM
[2023-06-28 16:01:55,400] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.28%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 16:01:55,415] [INFO] ===== Completeness check finished =====
[2023-06-28 16:01:55,415] [INFO] ===== Start GTDB Search =====
[2023-06-28 16:01:55,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019415205.1_ASM1941520v1_genomic.fna/markers.fasta)
[2023-06-28 16:01:55,416] [INFO] Task started: Blastn
[2023-06-28 16:01:55,416] [INFO] Running command: blastn -query GCA_019415205.1_ASM1941520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0e5b559-d3d0-4e11-be16-2a749e19324a/dqc_reference/reference_markers_gtdb.fasta -out GCA_019415205.1_ASM1941520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 16:01:56,630] [INFO] Task succeeded: Blastn
[2023-06-28 16:01:56,634] [INFO] Selected 12 target genomes.
[2023-06-28 16:01:56,634] [INFO] Target genome list was writen to GCA_019415205.1_ASM1941520v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 16:01:56,635] [INFO] Task started: fastANI
[2023-06-28 16:01:56,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg83760053-c0bb-42e5-ad5a-da15b2f91f8a/GCA_019415205.1_ASM1941520v1_genomic.fna.gz --refList GCA_019415205.1_ASM1941520v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019415205.1_ASM1941520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 16:02:03,888] [INFO] Task succeeded: fastANI
[2023-06-28 16:02:03,899] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 16:02:03,899] [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_010509575.1	s__Faecalibacterium prausnitzii_C	96.8008	670	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.30	96.44	0.84	0.71	49	conclusive
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	86.113	580	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.41	96.74	0.87	0.80	12	-
GCF_002549975.1	s__Faecalibacterium prausnitzii_H	85.8097	615	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCA_900539945.1	s__Faecalibacterium sp900539945	85.166	522	822	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_900539885.1	s__Faecalibacterium sp900539885	84.9816	503	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	84.9272	545	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	84.9081	552	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCF_003324185.1	s__Faecalibacterium prausnitzii	84.896	552	822	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	84.2567	541	822	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	84.2203	405	822	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_014858325.1	s__Faecalibacterium sp014858325	84.1856	366	822	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_900551435.1	s__Faecalibacterium sp900551435	83.8866	474	822	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.30	98.30	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-28 16:02:03,901] [INFO] GTDB search result was written to GCA_019415205.1_ASM1941520v1_genomic.fna/result_gtdb.tsv
[2023-06-28 16:02:03,902] [INFO] ===== GTDB Search completed =====
[2023-06-28 16:02:03,905] [INFO] DFAST_QC result json was written to GCA_019415205.1_ASM1941520v1_genomic.fna/dqc_result.json
[2023-06-28 16:02:03,905] [INFO] DFAST_QC completed!
[2023-06-28 16:02:03,905] [INFO] Total running time: 0h0m50s