[2024-01-24 13:09:43,419] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:43,421] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:43,421] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference
[2024-01-24 13:09:44,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:44,662] [INFO] Task started: Prodigal
[2024-01-24 13:09:44,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg3ed2fe25-d84f-4cd6-b81d-1636edac7804/GCF_000169155.1_ASM16915v1_genomic.fna.gz | prodigal -d GCF_000169155.1_ASM16915v1_genomic.fna/cds.fna -a GCF_000169155.1_ASM16915v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:52,142] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:52,142] [INFO] Task started: HMMsearch
[2024-01-24 13:09:52,143] [INFO] Running command: hmmsearch --tblout GCF_000169155.1_ASM16915v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/reference_markers.hmm GCF_000169155.1_ASM16915v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:52,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:52,417] [INFO] Found 6/6 markers.
[2024-01-24 13:09:52,442] [INFO] Query marker FASTA was written to GCF_000169155.1_ASM16915v1_genomic.fna/markers.fasta
[2024-01-24 13:09:52,442] [INFO] Task started: Blastn
[2024-01-24 13:09:52,443] [INFO] Running command: blastn -query GCF_000169155.1_ASM16915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/reference_markers.fasta -out GCF_000169155.1_ASM16915v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:53,118] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:53,123] [INFO] Selected 21 target genomes.
[2024-01-24 13:09:53,124] [INFO] Target genome list was writen to GCF_000169155.1_ASM16915v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:53,134] [INFO] Task started: fastANI
[2024-01-24 13:09:53,134] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed2fe25-d84f-4cd6-b81d-1636edac7804/GCF_000169155.1_ASM16915v1_genomic.fna.gz --refList GCF_000169155.1_ASM16915v1_genomic.fna/target_genomes.txt --output GCF_000169155.1_ASM16915v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:03,869] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:03,870] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:03,871] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:03,876] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:10:03,877] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:10:03,877] [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
Methylomusa anaerophila	strain=MMFC1	GCA_003966895.1	1930071	1930071	type	True	77.8293	66	939	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:03,879] [INFO] DFAST Taxonomy check result was written to GCF_000169155.1_ASM16915v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:03,880] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:03,880] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:03,880] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/checkm_data
[2024-01-24 13:10:03,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:03,914] [INFO] Task started: CheckM
[2024-01-24 13:10:03,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000169155.1_ASM16915v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000169155.1_ASM16915v1_genomic.fna/checkm_input GCF_000169155.1_ASM16915v1_genomic.fna/checkm_result
[2024-01-24 13:10:31,837] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:31,838] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:31,863] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:31,863] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:31,864] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000169155.1_ASM16915v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:31,865] [INFO] Task started: Blastn
[2024-01-24 13:10:31,865] [INFO] Running command: blastn -query GCF_000169155.1_ASM16915v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc643216-7a0e-4571-98f0-d61cd827f352/dqc_reference/reference_markers_gtdb.fasta -out GCF_000169155.1_ASM16915v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:32,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:32,724] [INFO] Selected 19 target genomes.
[2024-01-24 13:10:32,724] [INFO] Target genome list was writen to GCF_000169155.1_ASM16915v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:32,795] [INFO] Task started: fastANI
[2024-01-24 13:10:32,795] [INFO] Running command: fastANI --query /var/lib/cwl/stg3ed2fe25-d84f-4cd6-b81d-1636edac7804/GCF_000169155.1_ASM16915v1_genomic.fna.gz --refList GCF_000169155.1_ASM16915v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000169155.1_ASM16915v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:42,198] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:42,208] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:42,208] [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_000169155.1	s__Thermosinus carboxydivorans	100.0	938	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Thermosinus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900102435.1	s__Sporolituus thermophilus	90.7541	733	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Thermosinaceae;g__Sporolituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641255.1	s__Sporomusa termitida	78.062	64	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Sporomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966895.1	s__Methylomusa anaerophila	78.0208	66	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__Sporomusaceae;g__Methylomusa	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002482545.1	s__UBA7701 sp002482545	76.4898	69	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UBA7701;g__UBA7701	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018434945.1	s__SL1-B47 sp018434945	76.452	75	939	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Sporomusales;f__UBA7701;g__SL1-B47	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:42,210] [INFO] GTDB search result was written to GCF_000169155.1_ASM16915v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:42,211] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:42,213] [INFO] DFAST_QC result json was written to GCF_000169155.1_ASM16915v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:42,213] [INFO] DFAST_QC completed!
[2024-01-24 13:10:42,213] [INFO] Total running time: 0h0m59s