[2023-06-17 02:35:15,711] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:35:15,713] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:35:15,713] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference
[2023-06-17 02:35:16,905] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:35:16,911] [INFO] Task started: Prodigal
[2023-06-17 02:35:16,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg90ae672b-7193-4d09-a7db-7821b30edc7d/GCA_013333695.2_ASM1333369v2_genomic.fna.gz | prodigal -d GCA_013333695.2_ASM1333369v2_genomic.fna/cds.fna -a GCA_013333695.2_ASM1333369v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:35:18,887] [INFO] Task succeeded: Prodigal
[2023-06-17 02:35:18,888] [INFO] Task started: HMMsearch
[2023-06-17 02:35:18,888] [INFO] Running command: hmmsearch --tblout GCA_013333695.2_ASM1333369v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/reference_markers.hmm GCA_013333695.2_ASM1333369v2_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:35:19,075] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:35:19,076] [INFO] Found 6/6 markers.
[2023-06-17 02:35:19,104] [INFO] Query marker FASTA was written to GCA_013333695.2_ASM1333369v2_genomic.fna/markers.fasta
[2023-06-17 02:35:19,104] [INFO] Task started: Blastn
[2023-06-17 02:35:19,104] [INFO] Running command: blastn -query GCA_013333695.2_ASM1333369v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/reference_markers.fasta -out GCA_013333695.2_ASM1333369v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:35:19,825] [INFO] Task succeeded: Blastn
[2023-06-17 02:35:19,830] [INFO] Selected 17 target genomes.
[2023-06-17 02:35:19,830] [INFO] Target genome list was writen to GCA_013333695.2_ASM1333369v2_genomic.fna/target_genomes.txt
[2023-06-17 02:35:19,840] [INFO] Task started: fastANI
[2023-06-17 02:35:19,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ae672b-7193-4d09-a7db-7821b30edc7d/GCA_013333695.2_ASM1333369v2_genomic.fna.gz --refList GCA_013333695.2_ASM1333369v2_genomic.fna/target_genomes.txt --output GCA_013333695.2_ASM1333369v2_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:35:32,348] [INFO] Task succeeded: fastANI
[2023-06-17 02:35:32,349] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:35:32,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:35:32,351] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:35:32,351] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:35:32,351] [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
--------------------------------------------------------------------------------
[2023-06-17 02:35:32,353] [INFO] DFAST Taxonomy check result was written to GCA_013333695.2_ASM1333369v2_genomic.fna/tc_result.tsv
[2023-06-17 02:35:32,354] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:35:32,354] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:35:32,354] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/checkm_data
[2023-06-17 02:35:32,357] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:35:32,373] [INFO] Task started: CheckM
[2023-06-17 02:35:32,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013333695.2_ASM1333369v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013333695.2_ASM1333369v2_genomic.fna/checkm_input GCA_013333695.2_ASM1333369v2_genomic.fna/checkm_result
[2023-06-17 02:35:47,232] [INFO] Task succeeded: CheckM
[2023-06-17 02:35:47,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 84.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:35:47,253] [INFO] ===== Completeness check finished =====
[2023-06-17 02:35:47,253] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:35:47,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013333695.2_ASM1333369v2_genomic.fna/markers.fasta)
[2023-06-17 02:35:47,254] [INFO] Task started: Blastn
[2023-06-17 02:35:47,254] [INFO] Running command: blastn -query GCA_013333695.2_ASM1333369v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1ae40be-dfac-4231-be62-dd4d1637c7aa/dqc_reference/reference_markers_gtdb.fasta -out GCA_013333695.2_ASM1333369v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:35:48,229] [INFO] Task succeeded: Blastn
[2023-06-17 02:35:48,237] [INFO] Selected 14 target genomes.
[2023-06-17 02:35:48,238] [INFO] Target genome list was writen to GCA_013333695.2_ASM1333369v2_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:35:48,242] [INFO] Task started: fastANI
[2023-06-17 02:35:48,243] [INFO] Running command: fastANI --query /var/lib/cwl/stg90ae672b-7193-4d09-a7db-7821b30edc7d/GCA_013333695.2_ASM1333369v2_genomic.fna.gz --refList GCA_013333695.2_ASM1333369v2_genomic.fna/target_genomes_gtdb.txt --output GCA_013333695.2_ASM1333369v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:35:51,057] [INFO] Task succeeded: fastANI
[2023-06-17 02:35:51,069] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:35:51,070] [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_013333695.2	s__Nanosynbacter sp013333695	100.0	239	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_005697215.1	s__Nanosynbacter sp005697215	93.4941	223	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	97.45	96.66	0.93	0.93	4	-
GCA_013100805.1	s__Nanosynbacter sp013100805	93.4002	221	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010202645.1	s__Nanosynbacter sp010202645	93.3148	223	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	98.37	98.37	0.98	0.98	2	-
GCA_010202845.1	s__Nanosynbacter sp010202845	93.1029	223	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013099015.1	s__Nanosynbacter sp013099015	92.9363	220	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013099195.1	s__Nanosynbacter sp013099195	91.9296	221	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010202465.1	s__Nanosynbacter sp010202465	91.6963	216	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013100825.1	s__Nanosynbacter sp013100825	91.571	217	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	97.28	97.28	0.98	0.98	2	-
GCA_010202115.1	s__Nanosynbacter sp010202115	91.5633	211	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372305.1	s__Nanosynbacter sp905372305	84.1737	138	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905373795.1	s__Nanosynbacter sp905373795	83.7465	133	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372275.1	s__Saccharimonas sp905372275	80.5644	60	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333625.2	s__Saccharimonas sp013333625	80.3027	55	239	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:35:51,073] [INFO] GTDB search result was written to GCA_013333695.2_ASM1333369v2_genomic.fna/result_gtdb.tsv
[2023-06-17 02:35:51,073] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:35:51,077] [INFO] DFAST_QC result json was written to GCA_013333695.2_ASM1333369v2_genomic.fna/dqc_result.json
[2023-06-17 02:35:51,077] [INFO] DFAST_QC completed!
[2023-06-17 02:35:51,077] [INFO] Total running time: 0h0m35s