[2023-06-28 19:03:55,720] [INFO] DFAST_QC pipeline started.
[2023-06-28 19:03:55,722] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 19:03:55,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference
[2023-06-28 19:03:57,034] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 19:03:57,035] [INFO] Task started: Prodigal
[2023-06-28 19:03:57,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgec537ac9-6ca4-4683-aba5-fd652009e33a/GCA_017997735.1_ASM1799773v1_genomic.fna.gz | prodigal -d GCA_017997735.1_ASM1799773v1_genomic.fna/cds.fna -a GCA_017997735.1_ASM1799773v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 19:03:59,747] [INFO] Task succeeded: Prodigal
[2023-06-28 19:03:59,748] [INFO] Task started: HMMsearch
[2023-06-28 19:03:59,748] [INFO] Running command: hmmsearch --tblout GCA_017997735.1_ASM1799773v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/reference_markers.hmm GCA_017997735.1_ASM1799773v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 19:03:59,966] [INFO] Task succeeded: HMMsearch
[2023-06-28 19:03:59,967] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgec537ac9-6ca4-4683-aba5-fd652009e33a/GCA_017997735.1_ASM1799773v1_genomic.fna.gz]
[2023-06-28 19:03:59,988] [INFO] Query marker FASTA was written to GCA_017997735.1_ASM1799773v1_genomic.fna/markers.fasta
[2023-06-28 19:03:59,988] [INFO] Task started: Blastn
[2023-06-28 19:03:59,988] [INFO] Running command: blastn -query GCA_017997735.1_ASM1799773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/reference_markers.fasta -out GCA_017997735.1_ASM1799773v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:00,598] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:00,628] [INFO] Selected 18 target genomes.
[2023-06-28 19:04:00,628] [INFO] Target genome list was writen to GCA_017997735.1_ASM1799773v1_genomic.fna/target_genomes.txt
[2023-06-28 19:04:00,635] [INFO] Task started: fastANI
[2023-06-28 19:04:00,636] [INFO] Running command: fastANI --query /var/lib/cwl/stgec537ac9-6ca4-4683-aba5-fd652009e33a/GCA_017997735.1_ASM1799773v1_genomic.fna.gz --refList GCA_017997735.1_ASM1799773v1_genomic.fna/target_genomes.txt --output GCA_017997735.1_ASM1799773v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 19:04:11,320] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:11,320] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 19:04:11,321] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 19:04:11,325] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2023-06-28 19:04:11,325] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-28 19:04:11,325] [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
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	99.1954	291	353	95	conclusive
--------------------------------------------------------------------------------
[2023-06-28 19:04:11,327] [INFO] DFAST Taxonomy check result was written to GCA_017997735.1_ASM1799773v1_genomic.fna/tc_result.tsv
[2023-06-28 19:04:11,328] [INFO] ===== Taxonomy check completed =====
[2023-06-28 19:04:11,328] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 19:04:11,328] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/checkm_data
[2023-06-28 19:04:11,329] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 19:04:11,352] [INFO] Task started: CheckM
[2023-06-28 19:04:11,352] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017997735.1_ASM1799773v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017997735.1_ASM1799773v1_genomic.fna/checkm_input GCA_017997735.1_ASM1799773v1_genomic.fna/checkm_result
[2023-06-28 19:04:28,692] [INFO] Task succeeded: CheckM
[2023-06-28 19:04:28,694] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 19:04:28,718] [INFO] ===== Completeness check finished =====
[2023-06-28 19:04:28,718] [INFO] ===== Start GTDB Search =====
[2023-06-28 19:04:28,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017997735.1_ASM1799773v1_genomic.fna/markers.fasta)
[2023-06-28 19:04:28,719] [INFO] Task started: Blastn
[2023-06-28 19:04:28,719] [INFO] Running command: blastn -query GCA_017997735.1_ASM1799773v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg391f6da0-d0b9-468e-aec2-09dea0883796/dqc_reference/reference_markers_gtdb.fasta -out GCA_017997735.1_ASM1799773v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 19:04:29,443] [INFO] Task succeeded: Blastn
[2023-06-28 19:04:29,447] [INFO] Selected 17 target genomes.
[2023-06-28 19:04:29,447] [INFO] Target genome list was writen to GCA_017997735.1_ASM1799773v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 19:04:29,454] [INFO] Task started: fastANI
[2023-06-28 19:04:29,455] [INFO] Running command: fastANI --query /var/lib/cwl/stgec537ac9-6ca4-4683-aba5-fd652009e33a/GCA_017997735.1_ASM1799773v1_genomic.fna.gz --refList GCA_017997735.1_ASM1799773v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017997735.1_ASM1799773v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 19:04:37,648] [INFO] Task succeeded: fastANI
[2023-06-28 19:04:37,653] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 19:04:37,653] [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_000173975.1	s__Anaerobutyricum hallii	99.1954	291	353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.51	97.99	0.84	0.63	21	conclusive
GCF_900209925.1	s__Anaerobutyricum soehngenii	85.7169	259	353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	97.18	96.91	0.82	0.70	12	-
GCA_900016875.1	s__Anaerobutyricum stercoris	78.5322	58	353	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerobutyricum	95.0	98.34	98.09	0.89	0.78	6	-
--------------------------------------------------------------------------------
[2023-06-28 19:04:37,655] [INFO] GTDB search result was written to GCA_017997735.1_ASM1799773v1_genomic.fna/result_gtdb.tsv
[2023-06-28 19:04:37,656] [INFO] ===== GTDB Search completed =====
[2023-06-28 19:04:37,659] [INFO] DFAST_QC result json was written to GCA_017997735.1_ASM1799773v1_genomic.fna/dqc_result.json
[2023-06-28 19:04:37,659] [INFO] DFAST_QC completed!
[2023-06-28 19:04:37,659] [INFO] Total running time: 0h0m42s