[2023-06-17 04:56:49,100] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:56:49,110] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:56:49,110] [INFO] DQC Reference Directory: /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference
[2023-06-17 04:56:51,501] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:56:51,502] [INFO] Task started: Prodigal
[2023-06-17 04:56:51,502] [INFO] Running command: gunzip -c /var/lib/cwl/stg3dabc928-f407-4ceb-b2fb-295596f22a36/GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna.gz | prodigal -d GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/cds.fna -a GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:56:52,885] [INFO] Task succeeded: Prodigal
[2023-06-17 04:56:52,885] [INFO] Task started: HMMsearch
[2023-06-17 04:56:52,886] [INFO] Running command: hmmsearch --tblout GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/reference_markers.hmm GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:56:53,242] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:56:53,244] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3dabc928-f407-4ceb-b2fb-295596f22a36/GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna.gz]
[2023-06-17 04:56:53,259] [INFO] Query marker FASTA was written to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/markers.fasta
[2023-06-17 04:56:53,260] [INFO] Task started: Blastn
[2023-06-17 04:56:53,260] [INFO] Running command: blastn -query GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/reference_markers.fasta -out GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:56:56,783] [INFO] Task succeeded: Blastn
[2023-06-17 04:56:56,787] [INFO] Selected 5 target genomes.
[2023-06-17 04:56:56,787] [INFO] Target genome list was writen to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/target_genomes.txt
[2023-06-17 04:56:56,921] [INFO] Task started: fastANI
[2023-06-17 04:56:56,921] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dabc928-f407-4ceb-b2fb-295596f22a36/GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna.gz --refList GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/target_genomes.txt --output GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:56:59,527] [INFO] Task succeeded: fastANI
[2023-06-17 04:56:59,528] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:56:59,528] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:56:59,530] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:56:59,530] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 04:56:59,530] [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 04:56:59,532] [INFO] DFAST Taxonomy check result was written to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/tc_result.tsv
[2023-06-17 04:56:59,532] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:56:59,533] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:56:59,533] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/checkm_data
[2023-06-17 04:56:59,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:56:59,548] [INFO] Task started: CheckM
[2023-06-17 04:56:59,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/checkm_input GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/checkm_result
[2023-06-17 04:57:12,965] [INFO] Task succeeded: CheckM
[2023-06-17 04:57:12,966] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 37.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:57:12,984] [INFO] ===== Completeness check finished =====
[2023-06-17 04:57:12,985] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:57:12,985] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/markers.fasta)
[2023-06-17 04:57:12,985] [INFO] Task started: Blastn
[2023-06-17 04:57:12,986] [INFO] Running command: blastn -query GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/markers.fasta -db /var/lib/cwl/stg5e1ca5bb-3fca-4f75-b2c9-7f6336260d44/dqc_reference/reference_markers_gtdb.fasta -out GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:13,461] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:13,466] [INFO] Selected 8 target genomes.
[2023-06-17 04:57:13,466] [INFO] Target genome list was writen to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:57:13,475] [INFO] Task started: fastANI
[2023-06-17 04:57:13,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg3dabc928-f407-4ceb-b2fb-295596f22a36/GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna.gz --refList GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/target_genomes_gtdb.txt --output GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:57:14,803] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:14,811] [INFO] Found 8 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-17 04:57:14,811] [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_015257605.1	s__Saccharimonas sp015257605	95.086	129	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	95.21	95.21	0.72	0.72	2	inconclusive
GCA_013333625.2	s__Saccharimonas sp013333625	95.0778	149	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_905371595.1	s__Saccharimonas sp905371595	94.8748	145	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372275.1	s__Saccharimonas sp905372275	94.8297	163	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905365145.1	s__Saccharimonas sp905365145	94.6636	160	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013333845.2	s__Saccharimonas sp013333845	94.6019	141	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905372095.1	s__Saccharimonas sp905372095	94.574	163	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	95.37	95.31	0.90	0.88	4	-
GCA_013333795.2	s__Saccharimonas sp013333795	94.31	124	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Saccharimonadaceae;g__Saccharimonas	95.0	97.51	97.51	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-06-17 04:57:14,813] [INFO] GTDB search result was written to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/result_gtdb.tsv
[2023-06-17 04:57:14,814] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:57:14,817] [INFO] DFAST_QC result json was written to GCA_905372855.1_SRR9217428-mag-bin.11_genomic.fna/dqc_result.json
[2023-06-17 04:57:14,817] [INFO] DFAST_QC completed!
[2023-06-17 04:57:14,817] [INFO] Total running time: 0h0m26s