[2023-06-30 21:54:51,714] [INFO] DFAST_QC pipeline started.
[2023-06-30 21:54:51,718] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 21:54:51,718] [INFO] DQC Reference Directory: /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference
[2023-06-30 21:54:53,014] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 21:54:53,018] [INFO] Task started: Prodigal
[2023-06-30 21:54:53,019] [INFO] Running command: gunzip -c /var/lib/cwl/stgee40e711-3d36-4289-b3fe-cf32fcd82dfa/GCA_024404875.1_ASM2440487v1_genomic.fna.gz | prodigal -d GCA_024404875.1_ASM2440487v1_genomic.fna/cds.fna -a GCA_024404875.1_ASM2440487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 21:54:59,324] [INFO] Task succeeded: Prodigal
[2023-06-30 21:54:59,325] [INFO] Task started: HMMsearch
[2023-06-30 21:54:59,325] [INFO] Running command: hmmsearch --tblout GCA_024404875.1_ASM2440487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/reference_markers.hmm GCA_024404875.1_ASM2440487v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 21:54:59,615] [INFO] Task succeeded: HMMsearch
[2023-06-30 21:54:59,616] [INFO] Found 6/6 markers.
[2023-06-30 21:54:59,650] [INFO] Query marker FASTA was written to GCA_024404875.1_ASM2440487v1_genomic.fna/markers.fasta
[2023-06-30 21:54:59,650] [INFO] Task started: Blastn
[2023-06-30 21:54:59,650] [INFO] Running command: blastn -query GCA_024404875.1_ASM2440487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/reference_markers.fasta -out GCA_024404875.1_ASM2440487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:55:00,310] [INFO] Task succeeded: Blastn
[2023-06-30 21:55:00,315] [INFO] Selected 28 target genomes.
[2023-06-30 21:55:00,315] [INFO] Target genome list was writen to GCA_024404875.1_ASM2440487v1_genomic.fna/target_genomes.txt
[2023-06-30 21:55:00,320] [INFO] Task started: fastANI
[2023-06-30 21:55:00,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgee40e711-3d36-4289-b3fe-cf32fcd82dfa/GCA_024404875.1_ASM2440487v1_genomic.fna.gz --refList GCA_024404875.1_ASM2440487v1_genomic.fna/target_genomes.txt --output GCA_024404875.1_ASM2440487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 21:55:16,946] [INFO] Task succeeded: fastANI
[2023-06-30 21:55:16,946] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 21:55:16,947] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 21:55:16,950] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 21:55:16,950] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 21:55:16,950] [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 21:55:16,954] [INFO] DFAST Taxonomy check result was written to GCA_024404875.1_ASM2440487v1_genomic.fna/tc_result.tsv
[2023-06-30 21:55:16,955] [INFO] ===== Taxonomy check completed =====
[2023-06-30 21:55:16,956] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 21:55:16,956] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/checkm_data
[2023-06-30 21:55:16,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 21:55:16,985] [INFO] Task started: CheckM
[2023-06-30 21:55:16,985] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024404875.1_ASM2440487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024404875.1_ASM2440487v1_genomic.fna/checkm_input GCA_024404875.1_ASM2440487v1_genomic.fna/checkm_result
[2023-06-30 21:55:42,818] [INFO] Task succeeded: CheckM
[2023-06-30 21:55:42,820] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 21:55:42,844] [INFO] ===== Completeness check finished =====
[2023-06-30 21:55:42,844] [INFO] ===== Start GTDB Search =====
[2023-06-30 21:55:42,845] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024404875.1_ASM2440487v1_genomic.fna/markers.fasta)
[2023-06-30 21:55:42,845] [INFO] Task started: Blastn
[2023-06-30 21:55:42,845] [INFO] Running command: blastn -query GCA_024404875.1_ASM2440487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6481ee54-43d1-4d7c-83c3-cf9fe57bd51c/dqc_reference/reference_markers_gtdb.fasta -out GCA_024404875.1_ASM2440487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 21:55:43,952] [INFO] Task succeeded: Blastn
[2023-06-30 21:55:43,956] [INFO] Selected 11 target genomes.
[2023-06-30 21:55:43,956] [INFO] Target genome list was writen to GCA_024404875.1_ASM2440487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 21:55:43,968] [INFO] Task started: fastANI
[2023-06-30 21:55:43,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgee40e711-3d36-4289-b3fe-cf32fcd82dfa/GCA_024404875.1_ASM2440487v1_genomic.fna.gz --refList GCA_024404875.1_ASM2440487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024404875.1_ASM2440487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 21:55:50,783] [INFO] Task succeeded: fastANI
[2023-06-30 21:55:50,802] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 21:55:50,802] [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_002394125.1	s__Firm-04 sp002394125	87.67	562	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	98.26	96.88	0.90	0.87	3	-
GCA_001603005.1	s__Firm-04 sp001603005	80.0248	332	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	97.77	97.77	0.85	0.85	2	-
GCA_017550285.1	s__Firm-04 sp017550285	79.8624	402	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	97.92	97.78	0.88	0.87	4	-
GCA_001940925.1	s__Firm-04 sp001940925	79.7076	366	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	95.65	95.65	0.68	0.68	2	-
GCA_017523995.1	s__Firm-04 sp017523995	79.619	407	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545185.1	s__Firm-04 sp017545185	79.4975	362	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017427265.1	s__Firm-04 sp017427265	79.4038	352	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017540225.1	s__Firm-04 sp017540225	79.354	272	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017541275.1	s__Firm-04 sp017541275	79.2941	255	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016281125.1	s__Firm-04 sp016281125	79.0591	350	732	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Firm-04	95.0	95.42	95.42	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2023-06-30 21:55:50,805] [INFO] GTDB search result was written to GCA_024404875.1_ASM2440487v1_genomic.fna/result_gtdb.tsv
[2023-06-30 21:55:50,806] [INFO] ===== GTDB Search completed =====
[2023-06-30 21:55:50,809] [INFO] DFAST_QC result json was written to GCA_024404875.1_ASM2440487v1_genomic.fna/dqc_result.json
[2023-06-30 21:55:50,809] [INFO] DFAST_QC completed!
[2023-06-30 21:55:50,810] [INFO] Total running time: 0h0m59s