[2023-06-30 10:36:58,628] [INFO] DFAST_QC pipeline started.
[2023-06-30 10:36:58,631] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 10:36:58,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference
[2023-06-30 10:36:59,825] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 10:36:59,826] [INFO] Task started: Prodigal
[2023-06-30 10:36:59,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg94fc31c9-c2f1-4887-b5e6-b0310fb18bca/GCA_024698705.1_ASM2469870v1_genomic.fna.gz | prodigal -d GCA_024698705.1_ASM2469870v1_genomic.fna/cds.fna -a GCA_024698705.1_ASM2469870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 10:37:05,940] [INFO] Task succeeded: Prodigal
[2023-06-30 10:37:05,940] [INFO] Task started: HMMsearch
[2023-06-30 10:37:05,941] [INFO] Running command: hmmsearch --tblout GCA_024698705.1_ASM2469870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/reference_markers.hmm GCA_024698705.1_ASM2469870v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 10:37:06,191] [INFO] Task succeeded: HMMsearch
[2023-06-30 10:37:06,192] [INFO] Found 6/6 markers.
[2023-06-30 10:37:06,220] [INFO] Query marker FASTA was written to GCA_024698705.1_ASM2469870v1_genomic.fna/markers.fasta
[2023-06-30 10:37:06,221] [INFO] Task started: Blastn
[2023-06-30 10:37:06,221] [INFO] Running command: blastn -query GCA_024698705.1_ASM2469870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/reference_markers.fasta -out GCA_024698705.1_ASM2469870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:37:06,859] [INFO] Task succeeded: Blastn
[2023-06-30 10:37:06,864] [INFO] Selected 34 target genomes.
[2023-06-30 10:37:06,865] [INFO] Target genome list was writen to GCA_024698705.1_ASM2469870v1_genomic.fna/target_genomes.txt
[2023-06-30 10:37:06,870] [INFO] Task started: fastANI
[2023-06-30 10:37:06,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fc31c9-c2f1-4887-b5e6-b0310fb18bca/GCA_024698705.1_ASM2469870v1_genomic.fna.gz --refList GCA_024698705.1_ASM2469870v1_genomic.fna/target_genomes.txt --output GCA_024698705.1_ASM2469870v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 10:37:23,829] [INFO] Task succeeded: fastANI
[2023-06-30 10:37:23,830] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 10:37:23,830] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 10:37:23,832] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 10:37:23,833] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 10:37:23,833] [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
--------------------------------------------------------------------------------
[2023-06-30 10:37:23,835] [INFO] DFAST Taxonomy check result was written to GCA_024698705.1_ASM2469870v1_genomic.fna/tc_result.tsv
[2023-06-30 10:37:23,837] [INFO] ===== Taxonomy check completed =====
[2023-06-30 10:37:23,837] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 10:37:23,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/checkm_data
[2023-06-30 10:37:23,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 10:37:23,876] [INFO] Task started: CheckM
[2023-06-30 10:37:23,876] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024698705.1_ASM2469870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024698705.1_ASM2469870v1_genomic.fna/checkm_input GCA_024698705.1_ASM2469870v1_genomic.fna/checkm_result
[2023-06-30 10:37:49,030] [INFO] Task succeeded: CheckM
[2023-06-30 10:37:49,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 7.18%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 10:37:49,060] [INFO] ===== Completeness check finished =====
[2023-06-30 10:37:49,060] [INFO] ===== Start GTDB Search =====
[2023-06-30 10:37:49,061] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024698705.1_ASM2469870v1_genomic.fna/markers.fasta)
[2023-06-30 10:37:49,061] [INFO] Task started: Blastn
[2023-06-30 10:37:49,061] [INFO] Running command: blastn -query GCA_024698705.1_ASM2469870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg274fedb9-6700-4079-894d-b9e51cb46882/dqc_reference/reference_markers_gtdb.fasta -out GCA_024698705.1_ASM2469870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 10:37:50,111] [INFO] Task succeeded: Blastn
[2023-06-30 10:37:50,120] [INFO] Selected 25 target genomes.
[2023-06-30 10:37:50,120] [INFO] Target genome list was writen to GCA_024698705.1_ASM2469870v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 10:37:50,133] [INFO] Task started: fastANI
[2023-06-30 10:37:50,133] [INFO] Running command: fastANI --query /var/lib/cwl/stg94fc31c9-c2f1-4887-b5e6-b0310fb18bca/GCA_024698705.1_ASM2469870v1_genomic.fna.gz --refList GCA_024698705.1_ASM2469870v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024698705.1_ASM2469870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 10:38:02,304] [INFO] Task succeeded: fastANI
[2023-06-30 10:38:02,323] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 10:38:02,323] [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_016290615.1	s__UBA1712 sp016290615	78.8064	195	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789785.1	s__UBA1712 sp902789785	78.6241	168	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	97.67	97.20	0.85	0.79	3	-
GCA_017619635.1	s__UBA1712 sp017619635	78.4606	196	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016286035.1	s__UBA1712 sp016286035	78.396	186	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017961385.1	s__UBA1712 sp017961385	77.7232	130	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	98.30	98.30	0.76	0.76	2	-
GCA_002317175.1	s__UBA1712 sp002317175	77.4944	105	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783735.1	s__UBA1712 sp902783735	77.4508	123	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790275.1	s__UBA3766 sp902790275	77.4008	50	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3766	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235845.1	s__UBA1712 sp905235845	76.7318	67	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA1712	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905234595.1	s__XBB2008 sp905234595	76.4455	52	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBB2008	95.0	97.02	97.02	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2023-06-30 10:38:02,326] [INFO] GTDB search result was written to GCA_024698705.1_ASM2469870v1_genomic.fna/result_gtdb.tsv
[2023-06-30 10:38:02,327] [INFO] ===== GTDB Search completed =====
[2023-06-30 10:38:02,333] [INFO] DFAST_QC result json was written to GCA_024698705.1_ASM2469870v1_genomic.fna/dqc_result.json
[2023-06-30 10:38:02,333] [INFO] DFAST_QC completed!
[2023-06-30 10:38:02,334] [INFO] Total running time: 0h1m4s