[2023-06-27 17:41:05,489] [INFO] DFAST_QC pipeline started.
[2023-06-27 17:41:05,492] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 17:41:05,492] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference
[2023-06-27 17:41:08,718] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 17:41:08,719] [INFO] Task started: Prodigal
[2023-06-27 17:41:08,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg86ae9601-f56e-4c0f-a117-11ffc32c3814/GCA_002454045.1_ASM245404v1_genomic.fna.gz | prodigal -d GCA_002454045.1_ASM245404v1_genomic.fna/cds.fna -a GCA_002454045.1_ASM245404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 17:41:14,012] [INFO] Task succeeded: Prodigal
[2023-06-27 17:41:14,013] [INFO] Task started: HMMsearch
[2023-06-27 17:41:14,013] [INFO] Running command: hmmsearch --tblout GCA_002454045.1_ASM245404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/reference_markers.hmm GCA_002454045.1_ASM245404v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 17:41:14,308] [INFO] Task succeeded: HMMsearch
[2023-06-27 17:41:14,313] [INFO] Found 6/6 markers.
[2023-06-27 17:41:14,342] [INFO] Query marker FASTA was written to GCA_002454045.1_ASM245404v1_genomic.fna/markers.fasta
[2023-06-27 17:41:14,343] [INFO] Task started: Blastn
[2023-06-27 17:41:14,343] [INFO] Running command: blastn -query GCA_002454045.1_ASM245404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/reference_markers.fasta -out GCA_002454045.1_ASM245404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:15,089] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:15,093] [INFO] Selected 26 target genomes.
[2023-06-27 17:41:15,093] [INFO] Target genome list was writen to GCA_002454045.1_ASM245404v1_genomic.fna/target_genomes.txt
[2023-06-27 17:41:15,097] [INFO] Task started: fastANI
[2023-06-27 17:41:15,097] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ae9601-f56e-4c0f-a117-11ffc32c3814/GCA_002454045.1_ASM245404v1_genomic.fna.gz --refList GCA_002454045.1_ASM245404v1_genomic.fna/target_genomes.txt --output GCA_002454045.1_ASM245404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 17:41:34,209] [INFO] Task succeeded: fastANI
[2023-06-27 17:41:34,210] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 17:41:34,210] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 17:41:34,212] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 17:41:34,212] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-27 17:41:34,212] [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
--------------------------------------------------------------------------------
[2023-06-27 17:41:34,215] [INFO] DFAST Taxonomy check result was written to GCA_002454045.1_ASM245404v1_genomic.fna/tc_result.tsv
[2023-06-27 17:41:34,215] [INFO] ===== Taxonomy check completed =====
[2023-06-27 17:41:34,216] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 17:41:34,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/checkm_data
[2023-06-27 17:41:34,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 17:41:34,241] [INFO] Task started: CheckM
[2023-06-27 17:41:34,242] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002454045.1_ASM245404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002454045.1_ASM245404v1_genomic.fna/checkm_input GCA_002454045.1_ASM245404v1_genomic.fna/checkm_result
[2023-06-27 17:41:56,229] [INFO] Task succeeded: CheckM
[2023-06-27 17:41:56,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 17:41:56,262] [INFO] ===== Completeness check finished =====
[2023-06-27 17:41:56,262] [INFO] ===== Start GTDB Search =====
[2023-06-27 17:41:56,263] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002454045.1_ASM245404v1_genomic.fna/markers.fasta)
[2023-06-27 17:41:56,263] [INFO] Task started: Blastn
[2023-06-27 17:41:56,263] [INFO] Running command: blastn -query GCA_002454045.1_ASM245404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc72cb7-9ca3-4b79-be33-2c683b6fb57e/dqc_reference/reference_markers_gtdb.fasta -out GCA_002454045.1_ASM245404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 17:41:57,400] [INFO] Task succeeded: Blastn
[2023-06-27 17:41:57,412] [INFO] Selected 15 target genomes.
[2023-06-27 17:41:57,413] [INFO] Target genome list was writen to GCA_002454045.1_ASM245404v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 17:41:57,425] [INFO] Task started: fastANI
[2023-06-27 17:41:57,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg86ae9601-f56e-4c0f-a117-11ffc32c3814/GCA_002454045.1_ASM245404v1_genomic.fna.gz --refList GCA_002454045.1_ASM245404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002454045.1_ASM245404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 17:42:05,490] [INFO] Task succeeded: fastANI
[2023-06-27 17:42:05,501] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 17:42:05,501] [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_002454045.1	s__LS-NOB sp002454045	100.0	558	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_003545625.1	s__LS-NOB sp003545625	79.4415	279	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
GCA_018653085.1	s__LS-NOB sp018653085	79.0593	385	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_001542995.1	s__LS-NOB sp001542995	78.0485	324	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	77.2414	228	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_018673915.1	s__LS-NOB sp018673915	76.9305	203	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_018664975.1	s__LS-NOB sp018664975	76.7261	142	559	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 17:42:05,503] [INFO] GTDB search result was written to GCA_002454045.1_ASM245404v1_genomic.fna/result_gtdb.tsv
[2023-06-27 17:42:05,504] [INFO] ===== GTDB Search completed =====
[2023-06-27 17:42:05,507] [INFO] DFAST_QC result json was written to GCA_002454045.1_ASM245404v1_genomic.fna/dqc_result.json
[2023-06-27 17:42:05,507] [INFO] DFAST_QC completed!
[2023-06-27 17:42:05,507] [INFO] Total running time: 0h1m0s