[2024-01-25 17:43:50,721] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:43:50,722] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:43:50,722] [INFO] DQC Reference Directory: /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference
[2024-01-25 17:43:51,817] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:43:51,818] [INFO] Task started: Prodigal
[2024-01-25 17:43:51,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg694ebc04-229d-41dc-b96e-3ebf62529917/GCF_900086705.1_PRJEB13934_genomic.fna.gz | prodigal -d GCF_900086705.1_PRJEB13934_genomic.fna/cds.fna -a GCF_900086705.1_PRJEB13934_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:43:59,578] [INFO] Task succeeded: Prodigal
[2024-01-25 17:43:59,579] [INFO] Task started: HMMsearch
[2024-01-25 17:43:59,579] [INFO] Running command: hmmsearch --tblout GCF_900086705.1_PRJEB13934_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/reference_markers.hmm GCF_900086705.1_PRJEB13934_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:43:59,794] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:43:59,795] [INFO] Found 6/6 markers.
[2024-01-25 17:43:59,827] [INFO] Query marker FASTA was written to GCF_900086705.1_PRJEB13934_genomic.fna/markers.fasta
[2024-01-25 17:43:59,828] [INFO] Task started: Blastn
[2024-01-25 17:43:59,828] [INFO] Running command: blastn -query GCF_900086705.1_PRJEB13934_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/reference_markers.fasta -out GCF_900086705.1_PRJEB13934_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:00,360] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:00,363] [INFO] Selected 19 target genomes.
[2024-01-25 17:44:00,363] [INFO] Target genome list was writen to GCF_900086705.1_PRJEB13934_genomic.fna/target_genomes.txt
[2024-01-25 17:44:00,377] [INFO] Task started: fastANI
[2024-01-25 17:44:00,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg694ebc04-229d-41dc-b96e-3ebf62529917/GCF_900086705.1_PRJEB13934_genomic.fna.gz --refList GCF_900086705.1_PRJEB13934_genomic.fna/target_genomes.txt --output GCF_900086705.1_PRJEB13934_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:44:12,455] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:12,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:44:12,456] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:44:12,460] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:44:12,460] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:44:12,461] [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
Massilibacillus massiliensis	strain=Marseille-P2411	GCA_900086705.1	1806837	1806837	type	True	100.0	1331	1331	95	conclusive
Pelosinus fermentans	strain=R7	GCA_000271485.2	365349	365349	type	True	78.2395	91	1331	95	below_threshold
Pelorhabdus rhamnosifermentans	strain=BoRhaA	GCA_018835585.1	2772457	2772457	type	True	76.2885	63	1331	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:44:12,462] [INFO] DFAST Taxonomy check result was written to GCF_900086705.1_PRJEB13934_genomic.fna/tc_result.tsv
[2024-01-25 17:44:12,462] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:44:12,463] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:44:12,463] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/checkm_data
[2024-01-25 17:44:12,464] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:44:12,504] [INFO] Task started: CheckM
[2024-01-25 17:44:12,505] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900086705.1_PRJEB13934_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900086705.1_PRJEB13934_genomic.fna/checkm_input GCF_900086705.1_PRJEB13934_genomic.fna/checkm_result
[2024-01-25 17:44:39,586] [INFO] Task succeeded: CheckM
[2024-01-25 17:44:39,587] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:44:39,610] [INFO] ===== Completeness check finished =====
[2024-01-25 17:44:39,610] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:44:39,612] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900086705.1_PRJEB13934_genomic.fna/markers.fasta)
[2024-01-25 17:44:39,612] [INFO] Task started: Blastn
[2024-01-25 17:44:39,612] [INFO] Running command: blastn -query GCF_900086705.1_PRJEB13934_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c55c31-ed44-470e-bddf-1fda760f23b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900086705.1_PRJEB13934_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:44:40,414] [INFO] Task succeeded: Blastn
[2024-01-25 17:44:40,416] [INFO] Selected 21 target genomes.
[2024-01-25 17:44:40,417] [INFO] Target genome list was writen to GCF_900086705.1_PRJEB13934_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:44:40,437] [INFO] Task started: fastANI
[2024-01-25 17:44:40,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg694ebc04-229d-41dc-b96e-3ebf62529917/GCF_900086705.1_PRJEB13934_genomic.fna.gz --refList GCF_900086705.1_PRJEB13934_genomic.fna/target_genomes_gtdb.txt --output GCF_900086705.1_PRJEB13934_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:44:55,012] [INFO] Task succeeded: fastANI
[2024-01-25 17:44:55,018] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:44:55,018] [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_900086705.1	s__Massilibacillus massiliensis	100.0	1331	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__Massilibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902363205.1	s__CABIZH01 sp902363205	78.5238	172	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Selenomonadales;f__Massilibacillaceae;g__CABIZH01	95.0	97.61	97.54	0.87	0.81	4	-
GCF_000271665.2	s__Pelosinus fermentans_A	78.3947	98	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000271485.2	s__Pelosinus fermentans	78.3754	88	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	99.65	99.40	0.97	0.95	5	-
GCA_002434245.1	s__Pelosinus fermentans_B	76.8893	73	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__Pelosinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018835585.1	s__Pelorhabdus rhamnosifermentans	76.3167	62	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__UMGS1260;f__UMGS1260;g__Pelorhabdus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017889585.1	s__CTSoil-075 sp017889585	75.5668	54	1331	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Propionisporales;f__Propionisporaceae;g__CTSoil-075	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:44:55,020] [INFO] GTDB search result was written to GCF_900086705.1_PRJEB13934_genomic.fna/result_gtdb.tsv
[2024-01-25 17:44:55,020] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:44:55,023] [INFO] DFAST_QC result json was written to GCF_900086705.1_PRJEB13934_genomic.fna/dqc_result.json
[2024-01-25 17:44:55,023] [INFO] DFAST_QC completed!
[2024-01-25 17:44:55,023] [INFO] Total running time: 0h1m4s