[2024-01-24 11:12:28,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:28,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:28,034] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference
[2024-01-24 11:12:29,469] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:29,470] [INFO] Task started: Prodigal
[2024-01-24 11:12:29,470] [INFO] Running command: gunzip -c /var/lib/cwl/stgebde71bf-1db4-4d4c-91ea-d87b1a23ef4b/GCF_000160455.2_ASM16045v2_genomic.fna.gz | prodigal -d GCF_000160455.2_ASM16045v2_genomic.fna/cds.fna -a GCF_000160455.2_ASM16045v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:35,152] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:35,152] [INFO] Task started: HMMsearch
[2024-01-24 11:12:35,152] [INFO] Running command: hmmsearch --tblout GCF_000160455.2_ASM16045v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/reference_markers.hmm GCF_000160455.2_ASM16045v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:35,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:35,428] [INFO] Found 6/6 markers.
[2024-01-24 11:12:35,450] [INFO] Query marker FASTA was written to GCF_000160455.2_ASM16045v2_genomic.fna/markers.fasta
[2024-01-24 11:12:35,450] [INFO] Task started: Blastn
[2024-01-24 11:12:35,450] [INFO] Running command: blastn -query GCF_000160455.2_ASM16045v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/reference_markers.fasta -out GCF_000160455.2_ASM16045v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:36,096] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:36,099] [INFO] Selected 8 target genomes.
[2024-01-24 11:12:36,099] [INFO] Target genome list was writen to GCF_000160455.2_ASM16045v2_genomic.fna/target_genomes.txt
[2024-01-24 11:12:36,107] [INFO] Task started: fastANI
[2024-01-24 11:12:36,107] [INFO] Running command: fastANI --query /var/lib/cwl/stgebde71bf-1db4-4d4c-91ea-d87b1a23ef4b/GCF_000160455.2_ASM16045v2_genomic.fna.gz --refList GCF_000160455.2_ASM16045v2_genomic.fna/target_genomes.txt --output GCF_000160455.2_ASM16045v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:40,859] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:40,860] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:40,860] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:40,866] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:12:40,866] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:12:40,866] [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
Acetomicrobium hydrogeniformans	strain=OS1	GCA_000160455.2	649746	649746	type	True	100.0	705	705	95	inconclusive
Acetomicrobium thermoterrenum	strain=DSM 13490	GCA_900107215.1	1120986	1120986	type	True	96.8224	592	705	95	inconclusive
Acetomicrobium mobile	strain=DSM 13181	GCA_000266925.1	97477	97477	type	True	82.846	224	705	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:40,868] [INFO] DFAST Taxonomy check result was written to GCF_000160455.2_ASM16045v2_genomic.fna/tc_result.tsv
[2024-01-24 11:12:40,869] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:40,869] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:40,869] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/checkm_data
[2024-01-24 11:12:40,871] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:40,895] [INFO] Task started: CheckM
[2024-01-24 11:12:40,896] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000160455.2_ASM16045v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000160455.2_ASM16045v2_genomic.fna/checkm_input GCF_000160455.2_ASM16045v2_genomic.fna/checkm_result
[2024-01-24 11:13:04,325] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:04,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:04,351] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:04,352] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:04,352] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000160455.2_ASM16045v2_genomic.fna/markers.fasta)
[2024-01-24 11:13:04,353] [INFO] Task started: Blastn
[2024-01-24 11:13:04,353] [INFO] Running command: blastn -query GCF_000160455.2_ASM16045v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f841504-b6d2-4a0d-80e0-e61d3028dbe6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000160455.2_ASM16045v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:05,207] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:05,211] [INFO] Selected 8 target genomes.
[2024-01-24 11:13:05,211] [INFO] Target genome list was writen to GCF_000160455.2_ASM16045v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:05,218] [INFO] Task started: fastANI
[2024-01-24 11:13:05,219] [INFO] Running command: fastANI --query /var/lib/cwl/stgebde71bf-1db4-4d4c-91ea-d87b1a23ef4b/GCF_000160455.2_ASM16045v2_genomic.fna.gz --refList GCF_000160455.2_ASM16045v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000160455.2_ASM16045v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:09,406] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:09,414] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:09,414] [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_000160455.2	s__Acetomicrobium hydrogeniformans	100.0	705	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.8272	100.00	100.00	1.00	1.00	2	conclusive
GCF_900107215.1	s__Acetomicrobium thermoterrenum	96.8224	592	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.8272	97.07	97.07	0.93	0.93	2	-
GCA_002433005.1	s__Acetomicrobium sp002433005	95.8967	557	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.2563	N/A	N/A	N/A	N/A	1	-
GCA_002385485.1	s__Acetomicrobium sp002385485	95.5756	430	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	96.1959	98.11	96.55	0.85	0.83	3	-
GCA_900129645.1	s__Acetomicrobium flavidum	82.4912	216	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	95.0	98.26	98.17	0.90	0.88	3	-
GCA_012518015.1	s__Acetomicrobium sp012518015	78.4938	116	705	d__Bacteria;p__Synergistota;c__Synergistia;o__Synergistales;f__Acetomicrobiaceae;g__Acetomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:09,417] [INFO] GTDB search result was written to GCF_000160455.2_ASM16045v2_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:09,417] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:09,420] [INFO] DFAST_QC result json was written to GCF_000160455.2_ASM16045v2_genomic.fna/dqc_result.json
[2024-01-24 11:13:09,420] [INFO] DFAST_QC completed!
[2024-01-24 11:13:09,420] [INFO] Total running time: 0h0m41s