[2023-06-29 07:57:14,939] [INFO] DFAST_QC pipeline started.
[2023-06-29 07:57:14,943] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 07:57:14,943] [INFO] DQC Reference Directory: /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference
[2023-06-29 07:57:16,535] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 07:57:16,536] [INFO] Task started: Prodigal
[2023-06-29 07:57:16,536] [INFO] Running command: gunzip -c /var/lib/cwl/stg1812d018-740e-43be-8949-64f7f2ef0875/GCA_015233765.1_ASM1523376v1_genomic.fna.gz | prodigal -d GCA_015233765.1_ASM1523376v1_genomic.fna/cds.fna -a GCA_015233765.1_ASM1523376v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 07:57:24,379] [INFO] Task succeeded: Prodigal
[2023-06-29 07:57:24,380] [INFO] Task started: HMMsearch
[2023-06-29 07:57:24,380] [INFO] Running command: hmmsearch --tblout GCA_015233765.1_ASM1523376v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/reference_markers.hmm GCA_015233765.1_ASM1523376v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 07:57:24,573] [INFO] Task succeeded: HMMsearch
[2023-06-29 07:57:24,574] [INFO] Found 6/6 markers.
[2023-06-29 07:57:24,599] [INFO] Query marker FASTA was written to GCA_015233765.1_ASM1523376v1_genomic.fna/markers.fasta
[2023-06-29 07:57:24,599] [INFO] Task started: Blastn
[2023-06-29 07:57:24,599] [INFO] Running command: blastn -query GCA_015233765.1_ASM1523376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/reference_markers.fasta -out GCA_015233765.1_ASM1523376v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:57:25,165] [INFO] Task succeeded: Blastn
[2023-06-29 07:57:25,168] [INFO] Selected 18 target genomes.
[2023-06-29 07:57:25,169] [INFO] Target genome list was writen to GCA_015233765.1_ASM1523376v1_genomic.fna/target_genomes.txt
[2023-06-29 07:57:25,172] [INFO] Task started: fastANI
[2023-06-29 07:57:25,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg1812d018-740e-43be-8949-64f7f2ef0875/GCA_015233765.1_ASM1523376v1_genomic.fna.gz --refList GCA_015233765.1_ASM1523376v1_genomic.fna/target_genomes.txt --output GCA_015233765.1_ASM1523376v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 07:57:34,241] [INFO] Task succeeded: fastANI
[2023-06-29 07:57:34,242] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 07:57:34,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 07:57:34,244] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 07:57:34,244] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 07:57:34,244] [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
--------------------------------------------------------------------------------
[2023-06-29 07:57:34,246] [INFO] DFAST Taxonomy check result was written to GCA_015233765.1_ASM1523376v1_genomic.fna/tc_result.tsv
[2023-06-29 07:57:34,246] [INFO] ===== Taxonomy check completed =====
[2023-06-29 07:57:34,246] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 07:57:34,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/checkm_data
[2023-06-29 07:57:34,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 07:57:34,292] [INFO] Task started: CheckM
[2023-06-29 07:57:34,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015233765.1_ASM1523376v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015233765.1_ASM1523376v1_genomic.fna/checkm_input GCA_015233765.1_ASM1523376v1_genomic.fna/checkm_result
[2023-06-29 07:58:03,201] [INFO] Task succeeded: CheckM
[2023-06-29 07:58:03,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 07:58:03,217] [INFO] ===== Completeness check finished =====
[2023-06-29 07:58:03,217] [INFO] ===== Start GTDB Search =====
[2023-06-29 07:58:03,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015233765.1_ASM1523376v1_genomic.fna/markers.fasta)
[2023-06-29 07:58:03,218] [INFO] Task started: Blastn
[2023-06-29 07:58:03,218] [INFO] Running command: blastn -query GCA_015233765.1_ASM1523376v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge73b97a2-e47b-4cc6-8845-fc620f5d0d66/dqc_reference/reference_markers_gtdb.fasta -out GCA_015233765.1_ASM1523376v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 07:58:04,007] [INFO] Task succeeded: Blastn
[2023-06-29 07:58:04,011] [INFO] Selected 17 target genomes.
[2023-06-29 07:58:04,011] [INFO] Target genome list was writen to GCA_015233765.1_ASM1523376v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 07:58:04,016] [INFO] Task started: fastANI
[2023-06-29 07:58:04,016] [INFO] Running command: fastANI --query /var/lib/cwl/stg1812d018-740e-43be-8949-64f7f2ef0875/GCA_015233765.1_ASM1523376v1_genomic.fna.gz --refList GCA_015233765.1_ASM1523376v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015233765.1_ASM1523376v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 07:58:10,952] [INFO] Task succeeded: fastANI
[2023-06-29 07:58:10,960] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 07:58:10,960] [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_002753745.1	s__GCA-2753745 sp002753745	99.6546	642	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753745	95.0	99.68	99.68	0.89	0.89	2	conclusive
GCA_903908245.1	s__GCA-2753745 sp903908245	77.9459	210	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753745	95.0	99.88	99.87	0.96	0.95	3	-
GCA_015234065.1	s__JADFWS01 sp015234065	77.9178	68	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__JADFWS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015232565.1	s__GCA-2753745 sp015232565	77.7793	198	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753745	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015233705.1	s__JAAYZZ01 sp015233705	76.8096	55	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__JAAYZZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903860135.1	s__GCA-2753465 sp903860135	76.6026	69	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753465	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903901225.1	s__GCA-2753465 sp903901225	76.5112	79	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753465	95.0	99.99	99.98	0.98	0.96	7	-
GCA_903959815.1	s__GCA-2753465 sp903959815	75.929	69	880	d__Bacteria;p__Omnitrophota;c__Koll11;o__UBA10015;f__GCA-002753745;g__GCA-2753465	95.0	99.78	99.78	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-29 07:58:10,962] [INFO] GTDB search result was written to GCA_015233765.1_ASM1523376v1_genomic.fna/result_gtdb.tsv
[2023-06-29 07:58:10,963] [INFO] ===== GTDB Search completed =====
[2023-06-29 07:58:10,965] [INFO] DFAST_QC result json was written to GCA_015233765.1_ASM1523376v1_genomic.fna/dqc_result.json
[2023-06-29 07:58:10,965] [INFO] DFAST_QC completed!
[2023-06-29 07:58:10,965] [INFO] Total running time: 0h0m56s