[2023-06-18 18:31:20,091] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:20,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:20,093] [INFO] DQC Reference Directory: /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference
[2023-06-18 18:31:21,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:21,501] [INFO] Task started: Prodigal
[2023-06-18 18:31:21,501] [INFO] Running command: gunzip -c /var/lib/cwl/stgd37f4046-53c3-4b87-b3b3-a3a929791f99/GCA_014865765.1_ASM1486576v1_genomic.fna.gz | prodigal -d GCA_014865765.1_ASM1486576v1_genomic.fna/cds.fna -a GCA_014865765.1_ASM1486576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:27,817] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:27,817] [INFO] Task started: HMMsearch
[2023-06-18 18:31:27,817] [INFO] Running command: hmmsearch --tblout GCA_014865765.1_ASM1486576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/reference_markers.hmm GCA_014865765.1_ASM1486576v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:28,091] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:28,092] [INFO] Found 6/6 markers.
[2023-06-18 18:31:28,123] [INFO] Query marker FASTA was written to GCA_014865765.1_ASM1486576v1_genomic.fna/markers.fasta
[2023-06-18 18:31:28,124] [INFO] Task started: Blastn
[2023-06-18 18:31:28,124] [INFO] Running command: blastn -query GCA_014865765.1_ASM1486576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/reference_markers.fasta -out GCA_014865765.1_ASM1486576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:28,729] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:28,732] [INFO] Selected 25 target genomes.
[2023-06-18 18:31:28,733] [INFO] Target genome list was writen to GCA_014865765.1_ASM1486576v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:28,738] [INFO] Task started: fastANI
[2023-06-18 18:31:28,738] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37f4046-53c3-4b87-b3b3-a3a929791f99/GCA_014865765.1_ASM1486576v1_genomic.fna.gz --refList GCA_014865765.1_ASM1486576v1_genomic.fna/target_genomes.txt --output GCA_014865765.1_ASM1486576v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:45,984] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:45,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:45,985] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:45,992] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:31:45,992] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:31:45,992] [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
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	76.7411	62	758	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	76.6427	98	758	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	76.0408	79	758	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	76.0261	78	758	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:45,994] [INFO] DFAST Taxonomy check result was written to GCA_014865765.1_ASM1486576v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:45,995] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:45,995] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:45,995] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/checkm_data
[2023-06-18 18:31:45,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:46,062] [INFO] Task started: CheckM
[2023-06-18 18:31:46,062] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014865765.1_ASM1486576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014865765.1_ASM1486576v1_genomic.fna/checkm_input GCA_014865765.1_ASM1486576v1_genomic.fna/checkm_result
[2023-06-18 18:32:11,664] [INFO] Task succeeded: CheckM
[2023-06-18 18:32:11,665] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 18:32:11,689] [INFO] ===== Completeness check finished =====
[2023-06-18 18:32:11,690] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:32:11,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014865765.1_ASM1486576v1_genomic.fna/markers.fasta)
[2023-06-18 18:32:11,691] [INFO] Task started: Blastn
[2023-06-18 18:32:11,691] [INFO] Running command: blastn -query GCA_014865765.1_ASM1486576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd11442d9-2590-4ab2-808a-351207205542/dqc_reference/reference_markers_gtdb.fasta -out GCA_014865765.1_ASM1486576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:32:12,536] [INFO] Task succeeded: Blastn
[2023-06-18 18:32:12,541] [INFO] Selected 9 target genomes.
[2023-06-18 18:32:12,541] [INFO] Target genome list was writen to GCA_014865765.1_ASM1486576v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:32:12,545] [INFO] Task started: fastANI
[2023-06-18 18:32:12,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgd37f4046-53c3-4b87-b3b3-a3a929791f99/GCA_014865765.1_ASM1486576v1_genomic.fna.gz --refList GCA_014865765.1_ASM1486576v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014865765.1_ASM1486576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:32:17,816] [INFO] Task succeeded: fastANI
[2023-06-18 18:32:17,829] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:32:17,830] [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
GCA_003584705.1	s__Acetatifactor sp900066565	98.1862	693	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	conclusive
GCA_900772845.1	s__Acetatifactor sp900772845	89.4364	586	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_900771995.1	s__Acetatifactor sp900771995	88.6568	570	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447295.1	s__Acetatifactor sp003447295	88.2484	437	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	-
GCF_009695995.1	s__Acetatifactor intestinalis	88.0416	560	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	-
GCA_002431915.1	s__Acetatifactor sp002431915	86.4601	525	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766575.1	s__Acetatifactor sp900766575	86.0504	385	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056975.1	s__Acetatifactor sp015056975	77.5572	105	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303085.1	s__Acetatifactor sp016303085	76.9668	102	758	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:32:17,831] [INFO] GTDB search result was written to GCA_014865765.1_ASM1486576v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:32:17,832] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:32:17,835] [INFO] DFAST_QC result json was written to GCA_014865765.1_ASM1486576v1_genomic.fna/dqc_result.json
[2023-06-18 18:32:17,835] [INFO] DFAST_QC completed!
[2023-06-18 18:32:17,835] [INFO] Total running time: 0h0m58s