[2023-06-13 20:44:20,615] [INFO] DFAST_QC pipeline started.
[2023-06-13 20:44:20,616] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 20:44:20,616] [INFO] DQC Reference Directory: /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference
[2023-06-13 20:44:21,769] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 20:44:21,769] [INFO] Task started: Prodigal
[2023-06-13 20:44:21,770] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a4391de-9a68-4883-b918-568e0272f2db/GCA_022744685.1_ASM2274468v1_genomic.fna.gz | prodigal -d GCA_022744685.1_ASM2274468v1_genomic.fna/cds.fna -a GCA_022744685.1_ASM2274468v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 20:44:25,903] [INFO] Task succeeded: Prodigal
[2023-06-13 20:44:25,904] [INFO] Task started: HMMsearch
[2023-06-13 20:44:25,904] [INFO] Running command: hmmsearch --tblout GCA_022744685.1_ASM2274468v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/reference_markers.hmm GCA_022744685.1_ASM2274468v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 20:44:26,056] [INFO] Task succeeded: HMMsearch
[2023-06-13 20:44:26,057] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a4391de-9a68-4883-b918-568e0272f2db/GCA_022744685.1_ASM2274468v1_genomic.fna.gz]
[2023-06-13 20:44:26,087] [INFO] Query marker FASTA was written to GCA_022744685.1_ASM2274468v1_genomic.fna/markers.fasta
[2023-06-13 20:44:26,087] [INFO] Task started: Blastn
[2023-06-13 20:44:26,087] [INFO] Running command: blastn -query GCA_022744685.1_ASM2274468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/reference_markers.fasta -out GCA_022744685.1_ASM2274468v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:26,611] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:26,615] [INFO] Selected 6 target genomes.
[2023-06-13 20:44:26,615] [INFO] Target genome list was writen to GCA_022744685.1_ASM2274468v1_genomic.fna/target_genomes.txt
[2023-06-13 20:44:26,616] [INFO] Task started: fastANI
[2023-06-13 20:44:26,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a4391de-9a68-4883-b918-568e0272f2db/GCA_022744685.1_ASM2274468v1_genomic.fna.gz --refList GCA_022744685.1_ASM2274468v1_genomic.fna/target_genomes.txt --output GCA_022744685.1_ASM2274468v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 20:44:29,453] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:29,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 20:44:29,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 20:44:29,460] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 20:44:29,460] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 20:44:29,460] [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	85.2906	203	272	95	below_threshold
Faecalibacterium duncaniae	strain=JCM 31915	GCA_010509575.1	411483	411483	type	True	84.5128	186	272	95	below_threshold
Faecalibacterium duncaniae	strain=A2-165	GCA_000162015.1	411483	411483	type	True	84.4765	185	272	95	below_threshold
Faecalibacterium prausnitzii	strain=ATCC 27768	GCA_003324185.1	853	853	suspected-type	True	84.1507	198	272	95	below_threshold
Faecalibacterium gallinarum	strain=JCM 17207	GCA_022180365.1	2903556	2903556	type	True	81.0016	134	272	95	below_threshold
Subdoligranulum variabile	strain=DSM 15176	GCA_025152575.1	214851	214851	type	True	78.3452	54	272	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 20:44:29,461] [INFO] DFAST Taxonomy check result was written to GCA_022744685.1_ASM2274468v1_genomic.fna/tc_result.tsv
[2023-06-13 20:44:29,462] [INFO] ===== Taxonomy check completed =====
[2023-06-13 20:44:29,462] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 20:44:29,462] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/checkm_data
[2023-06-13 20:44:29,463] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 20:44:29,489] [INFO] Task started: CheckM
[2023-06-13 20:44:29,489] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022744685.1_ASM2274468v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022744685.1_ASM2274468v1_genomic.fna/checkm_input GCA_022744685.1_ASM2274468v1_genomic.fna/checkm_result
[2023-06-13 20:44:46,862] [INFO] Task succeeded: CheckM
[2023-06-13 20:44:46,863] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 20:44:46,878] [INFO] ===== Completeness check finished =====
[2023-06-13 20:44:46,879] [INFO] ===== Start GTDB Search =====
[2023-06-13 20:44:46,879] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022744685.1_ASM2274468v1_genomic.fna/markers.fasta)
[2023-06-13 20:44:46,879] [INFO] Task started: Blastn
[2023-06-13 20:44:46,879] [INFO] Running command: blastn -query GCA_022744685.1_ASM2274468v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8bf7a047-0f96-4ba0-a9bf-73ad0988cf8e/dqc_reference/reference_markers_gtdb.fasta -out GCA_022744685.1_ASM2274468v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 20:44:47,645] [INFO] Task succeeded: Blastn
[2023-06-13 20:44:47,648] [INFO] Selected 10 target genomes.
[2023-06-13 20:44:47,648] [INFO] Target genome list was writen to GCA_022744685.1_ASM2274468v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 20:44:47,649] [INFO] Task started: fastANI
[2023-06-13 20:44:47,649] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a4391de-9a68-4883-b918-568e0272f2db/GCA_022744685.1_ASM2274468v1_genomic.fna.gz --refList GCA_022744685.1_ASM2274468v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022744685.1_ASM2274468v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 20:44:51,663] [INFO] Task succeeded: fastANI
[2023-06-13 20:44:51,670] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 20:44:51,670] [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	95.5173	211	272	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	90.8867	184	272	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	86.7063	157	272	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_002549975.1	s__Faecalibacterium prausnitzii_H	85.0746	197	272	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_002550035.1	s__Faecalibacterium prausnitzii_E	85.0271	196	272	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_003287495.1	s__Faecalibacterium prausnitzii_I	84.8871	190	272	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.17	97.28	0.90	0.84	9	-
GCA_900539945.1	s__Faecalibacterium sp900539945	84.586	166	272	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	98.71	98.00	0.92	0.86	4	-
GCF_002549775.1	s__Faecalibacterium prausnitzii_F	84.2507	185	272	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.99	97.71	0.95	0.94	3	-
GCA_014858325.1	s__Faecalibacterium sp014858325	84.2219	136	272	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_900539885.1	s__Faecalibacterium sp900539885	83.9566	163	272	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Faecalibacterium	95.0	97.54	97.23	0.89	0.84	6	-
--------------------------------------------------------------------------------
[2023-06-13 20:44:51,672] [INFO] GTDB search result was written to GCA_022744685.1_ASM2274468v1_genomic.fna/result_gtdb.tsv
[2023-06-13 20:44:51,672] [INFO] ===== GTDB Search completed =====
[2023-06-13 20:44:51,676] [INFO] DFAST_QC result json was written to GCA_022744685.1_ASM2274468v1_genomic.fna/dqc_result.json
[2023-06-13 20:44:51,676] [INFO] DFAST_QC completed!
[2023-06-13 20:44:51,676] [INFO] Total running time: 0h0m31s