[2023-06-17 02:43:52,494] [INFO] DFAST_QC pipeline started.
[2023-06-17 02:43:52,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 02:43:52,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference
[2023-06-17 02:43:53,875] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 02:43:53,876] [INFO] Task started: Prodigal
[2023-06-17 02:43:53,877] [INFO] Running command: gunzip -c /var/lib/cwl/stge402c0f7-9255-498e-9de4-3a2a7d693070/GCA_009874385.1_ASM987438v1_genomic.fna.gz | prodigal -d GCA_009874385.1_ASM987438v1_genomic.fna/cds.fna -a GCA_009874385.1_ASM987438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 02:44:00,253] [INFO] Task succeeded: Prodigal
[2023-06-17 02:44:00,253] [INFO] Task started: HMMsearch
[2023-06-17 02:44:00,253] [INFO] Running command: hmmsearch --tblout GCA_009874385.1_ASM987438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/reference_markers.hmm GCA_009874385.1_ASM987438v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 02:44:00,453] [INFO] Task succeeded: HMMsearch
[2023-06-17 02:44:00,454] [INFO] Found 6/6 markers.
[2023-06-17 02:44:00,479] [INFO] Query marker FASTA was written to GCA_009874385.1_ASM987438v1_genomic.fna/markers.fasta
[2023-06-17 02:44:00,480] [INFO] Task started: Blastn
[2023-06-17 02:44:00,480] [INFO] Running command: blastn -query GCA_009874385.1_ASM987438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/reference_markers.fasta -out GCA_009874385.1_ASM987438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:01,079] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:01,082] [INFO] Selected 23 target genomes.
[2023-06-17 02:44:01,083] [INFO] Target genome list was writen to GCA_009874385.1_ASM987438v1_genomic.fna/target_genomes.txt
[2023-06-17 02:44:01,086] [INFO] Task started: fastANI
[2023-06-17 02:44:01,086] [INFO] Running command: fastANI --query /var/lib/cwl/stge402c0f7-9255-498e-9de4-3a2a7d693070/GCA_009874385.1_ASM987438v1_genomic.fna.gz --refList GCA_009874385.1_ASM987438v1_genomic.fna/target_genomes.txt --output GCA_009874385.1_ASM987438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 02:44:12,700] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:12,700] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 02:44:12,700] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 02:44:12,702] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 02:44:12,702] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 02:44:12,702] [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 02:44:12,704] [INFO] DFAST Taxonomy check result was written to GCA_009874385.1_ASM987438v1_genomic.fna/tc_result.tsv
[2023-06-17 02:44:12,705] [INFO] ===== Taxonomy check completed =====
[2023-06-17 02:44:12,705] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 02:44:12,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/checkm_data
[2023-06-17 02:44:12,708] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 02:44:12,735] [INFO] Task started: CheckM
[2023-06-17 02:44:12,735] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009874385.1_ASM987438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009874385.1_ASM987438v1_genomic.fna/checkm_input GCA_009874385.1_ASM987438v1_genomic.fna/checkm_result
[2023-06-17 02:44:37,451] [INFO] Task succeeded: CheckM
[2023-06-17 02:44:37,452] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 02:44:37,471] [INFO] ===== Completeness check finished =====
[2023-06-17 02:44:37,472] [INFO] ===== Start GTDB Search =====
[2023-06-17 02:44:37,472] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009874385.1_ASM987438v1_genomic.fna/markers.fasta)
[2023-06-17 02:44:37,472] [INFO] Task started: Blastn
[2023-06-17 02:44:37,472] [INFO] Running command: blastn -query GCA_009874385.1_ASM987438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd95f9e93-01c5-4595-af29-923f9c24d343/dqc_reference/reference_markers_gtdb.fasta -out GCA_009874385.1_ASM987438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 02:44:38,447] [INFO] Task succeeded: Blastn
[2023-06-17 02:44:38,450] [INFO] Selected 19 target genomes.
[2023-06-17 02:44:38,450] [INFO] Target genome list was writen to GCA_009874385.1_ASM987438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 02:44:38,459] [INFO] Task started: fastANI
[2023-06-17 02:44:38,459] [INFO] Running command: fastANI --query /var/lib/cwl/stge402c0f7-9255-498e-9de4-3a2a7d693070/GCA_009874385.1_ASM987438v1_genomic.fna.gz --refList GCA_009874385.1_ASM987438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009874385.1_ASM987438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 02:44:46,036] [INFO] Task succeeded: fastANI
[2023-06-17 02:44:46,046] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 02:44:46,046] [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_009873655.1	s__UBA8687 sp009873655	99.3718	758	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	conclusive
GCA_009873635.1	s__LS-NOB sp009873635	78.5122	141	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_018665625.1	s__UBA8687 sp018665625	77.8677	306	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013349585.1	s__UBA8687 sp013349585	77.5974	259	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697825.1	s__UBA8687 sp002697825	76.8959	148	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	76.6034	98	854	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_001542995.1	s__LS-NOB sp001542995	76.5791	127	854	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_002786505.1	s__LS-NOB sp002786505	76.407	85	854	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_018653085.1	s__LS-NOB sp018653085	76.3821	134	854	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_018702695.1	s__LS-NOB sp018702695	76.0785	72	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.34	99.32	0.82	0.80	4	-
GCA_018664975.1	s__LS-NOB sp018664975	75.6417	67	854	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 02:44:46,049] [INFO] GTDB search result was written to GCA_009874385.1_ASM987438v1_genomic.fna/result_gtdb.tsv
[2023-06-17 02:44:46,049] [INFO] ===== GTDB Search completed =====
[2023-06-17 02:44:46,052] [INFO] DFAST_QC result json was written to GCA_009874385.1_ASM987438v1_genomic.fna/dqc_result.json
[2023-06-17 02:44:46,052] [INFO] DFAST_QC completed!
[2023-06-17 02:44:46,052] [INFO] Total running time: 0h0m54s