[2023-06-13 08:52:08,532] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:52:08,536] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:52:08,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference
[2023-06-13 08:52:09,752] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:52:09,752] [INFO] Task started: Prodigal
[2023-06-13 08:52:09,753] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1213f26-43a9-4db9-a112-bf86a3a47f2f/GCA_022732065.1_ASM2273206v1_genomic.fna.gz | prodigal -d GCA_022732065.1_ASM2273206v1_genomic.fna/cds.fna -a GCA_022732065.1_ASM2273206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:16,362] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:16,362] [INFO] Task started: HMMsearch
[2023-06-13 08:52:16,362] [INFO] Running command: hmmsearch --tblout GCA_022732065.1_ASM2273206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/reference_markers.hmm GCA_022732065.1_ASM2273206v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:16,648] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:16,650] [INFO] Found 6/6 markers.
[2023-06-13 08:52:16,684] [INFO] Query marker FASTA was written to GCA_022732065.1_ASM2273206v1_genomic.fna/markers.fasta
[2023-06-13 08:52:16,685] [INFO] Task started: Blastn
[2023-06-13 08:52:16,685] [INFO] Running command: blastn -query GCA_022732065.1_ASM2273206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/reference_markers.fasta -out GCA_022732065.1_ASM2273206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:17,403] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:17,406] [INFO] Selected 7 target genomes.
[2023-06-13 08:52:17,407] [INFO] Target genome list was writen to GCA_022732065.1_ASM2273206v1_genomic.fna/target_genomes.txt
[2023-06-13 08:52:17,408] [INFO] Task started: fastANI
[2023-06-13 08:52:17,408] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1213f26-43a9-4db9-a112-bf86a3a47f2f/GCA_022732065.1_ASM2273206v1_genomic.fna.gz --refList GCA_022732065.1_ASM2273206v1_genomic.fna/target_genomes.txt --output GCA_022732065.1_ASM2273206v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:21,424] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:21,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:21,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:21,432] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 08:52:21,433] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 08:52:21,433] [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 hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	85.4567	484	657	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.859	446	657	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.7688	458	657	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	84.1426	458	657	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.8963	328	657	95	below_threshold
Fournierella massiliensis	strain=DSM 100451	GCA_004345265.1	1650663	1650663	type	True	78.0371	163	657	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	77.3474	59	657	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:21,435] [INFO] DFAST Taxonomy check result was written to GCA_022732065.1_ASM2273206v1_genomic.fna/tc_result.tsv
[2023-06-13 08:52:21,435] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:21,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:21,436] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/checkm_data
[2023-06-13 08:52:21,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:21,465] [INFO] Task started: CheckM
[2023-06-13 08:52:21,466] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022732065.1_ASM2273206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022732065.1_ASM2273206v1_genomic.fna/checkm_input GCA_022732065.1_ASM2273206v1_genomic.fna/checkm_result
[2023-06-13 08:52:47,096] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:47,098] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:47,122] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:47,122] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:47,123] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022732065.1_ASM2273206v1_genomic.fna/markers.fasta)
[2023-06-13 08:52:47,123] [INFO] Task started: Blastn
[2023-06-13 08:52:47,123] [INFO] Running command: blastn -query GCA_022732065.1_ASM2273206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg625d1a2f-8a87-4845-998b-7138a96bcf0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022732065.1_ASM2273206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:48,349] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:48,353] [INFO] Selected 12 target genomes.
[2023-06-13 08:52:48,353] [INFO] Target genome list was writen to GCA_022732065.1_ASM2273206v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:48,359] [INFO] Task started: fastANI
[2023-06-13 08:52:48,360] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1213f26-43a9-4db9-a112-bf86a3a47f2f/GCA_022732065.1_ASM2273206v1_genomic.fna.gz --refList GCA_022732065.1_ASM2273206v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022732065.1_ASM2273206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:52:54,977] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:54,992] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:52:54,992] [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_003293635.1	s__Faecalibacterium prausnitzii_G	96.1067	540	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.11	95.97	0.86	0.76	34	conclusive
GCA_900758465.1	s__Faecalibacterium sp900758465	91.1076	478	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.14	97.85	0.88	0.87	4	-
GCA_002313795.1	s__Faecalibacterium prausnitzii_L	86.3081	367	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.80	98.80	0.73	0.73	2	-
GCF_002550035.1	s__Faecalibacterium prausnitzii_E	85.7393	477	657	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	85.5944	482	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.03	97.77	0.90	0.86	9	-
GCF_003287495.1	s__Faecalibacterium prausnitzii_I	85.2021	470	657	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	84.772	455	657	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_003287405.1	s__Faecalibacterium prausnitzii_J	84.7477	450	657	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_900539945.1	s__Faecalibacterium sp900539945	84.7367	418	657	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_014858325.1	s__Faecalibacterium sp014858325	84.7295	319	657	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	84.0212	376	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.30	98.30	0.83	0.83	2	-
GCA_905215595.1	s__Faecalibacterium sp905215595	82.8779	322	657	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:52:54,994] [INFO] GTDB search result was written to GCA_022732065.1_ASM2273206v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:52:54,995] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:52:54,998] [INFO] DFAST_QC result json was written to GCA_022732065.1_ASM2273206v1_genomic.fna/dqc_result.json
[2023-06-13 08:52:54,998] [INFO] DFAST_QC completed!
[2023-06-13 08:52:54,998] [INFO] Total running time: 0h0m46s