[2023-06-19 06:07:19,754] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:07:19,758] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:07:19,758] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference
[2023-06-19 06:07:21,059] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:07:21,060] [INFO] Task started: Prodigal
[2023-06-19 06:07:21,060] [INFO] Running command: gunzip -c /var/lib/cwl/stg1f5d5bcd-7e9f-444c-a3c3-f7187e2d4455/GCA_018694935.1_ASM1869493v1_genomic.fna.gz | prodigal -d GCA_018694935.1_ASM1869493v1_genomic.fna/cds.fna -a GCA_018694935.1_ASM1869493v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:07:28,359] [INFO] Task succeeded: Prodigal
[2023-06-19 06:07:28,360] [INFO] Task started: HMMsearch
[2023-06-19 06:07:28,360] [INFO] Running command: hmmsearch --tblout GCA_018694935.1_ASM1869493v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/reference_markers.hmm GCA_018694935.1_ASM1869493v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:07:28,612] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:07:28,614] [INFO] Found 6/6 markers.
[2023-06-19 06:07:28,656] [INFO] Query marker FASTA was written to GCA_018694935.1_ASM1869493v1_genomic.fna/markers.fasta
[2023-06-19 06:07:28,657] [INFO] Task started: Blastn
[2023-06-19 06:07:28,657] [INFO] Running command: blastn -query GCA_018694935.1_ASM1869493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/reference_markers.fasta -out GCA_018694935.1_ASM1869493v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:07:29,275] [INFO] Task succeeded: Blastn
[2023-06-19 06:07:29,280] [INFO] Selected 24 target genomes.
[2023-06-19 06:07:29,281] [INFO] Target genome list was writen to GCA_018694935.1_ASM1869493v1_genomic.fna/target_genomes.txt
[2023-06-19 06:07:29,283] [INFO] Task started: fastANI
[2023-06-19 06:07:29,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5d5bcd-7e9f-444c-a3c3-f7187e2d4455/GCA_018694935.1_ASM1869493v1_genomic.fna.gz --refList GCA_018694935.1_ASM1869493v1_genomic.fna/target_genomes.txt --output GCA_018694935.1_ASM1869493v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:07:42,581] [INFO] Task succeeded: fastANI
[2023-06-19 06:07:42,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:07:42,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:07:42,586] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:07:42,586] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 06:07:42,586] [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
--------------------------------------------------------------------------------
[2023-06-19 06:07:42,589] [INFO] DFAST Taxonomy check result was written to GCA_018694935.1_ASM1869493v1_genomic.fna/tc_result.tsv
[2023-06-19 06:07:42,589] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:07:42,590] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:07:42,590] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/checkm_data
[2023-06-19 06:07:42,594] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:07:42,632] [INFO] Task started: CheckM
[2023-06-19 06:07:42,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018694935.1_ASM1869493v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018694935.1_ASM1869493v1_genomic.fna/checkm_input GCA_018694935.1_ASM1869493v1_genomic.fna/checkm_result
[2023-06-19 06:08:10,921] [INFO] Task succeeded: CheckM
[2023-06-19 06:08:10,923] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-19 06:08:10,954] [INFO] ===== Completeness check finished =====
[2023-06-19 06:08:10,955] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:08:10,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018694935.1_ASM1869493v1_genomic.fna/markers.fasta)
[2023-06-19 06:08:10,955] [INFO] Task started: Blastn
[2023-06-19 06:08:10,955] [INFO] Running command: blastn -query GCA_018694935.1_ASM1869493v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5015e26-2d0d-46e6-a573-ed6bc7c8e0a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_018694935.1_ASM1869493v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:08:11,962] [INFO] Task succeeded: Blastn
[2023-06-19 06:08:11,968] [INFO] Selected 10 target genomes.
[2023-06-19 06:08:11,968] [INFO] Target genome list was writen to GCA_018694935.1_ASM1869493v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:08:11,969] [INFO] Task started: fastANI
[2023-06-19 06:08:11,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg1f5d5bcd-7e9f-444c-a3c3-f7187e2d4455/GCA_018694935.1_ASM1869493v1_genomic.fna.gz --refList GCA_018694935.1_ASM1869493v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018694935.1_ASM1869493v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:08:17,357] [INFO] Task succeeded: fastANI
[2023-06-19 06:08:17,370] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:08:17,371] [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_018653085.1	s__LS-NOB sp018653085	99.793	806	871	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	conclusive
GCA_003545625.1	s__LS-NOB sp003545625	86.4527	412	871	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_001542995.1	s__LS-NOB sp001542995	81.393	536	871	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	80.5086	523	871	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	79.9738	552	871	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_002786505.1	s__LS-NOB sp002786505	79.9566	378	871	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_018664975.1	s__LS-NOB sp018664975	79.3529	418	871	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_002454045.1	s__LS-NOB sp002454045	78.9193	323	871	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.99	99.99	0.99	0.99	2	-
GCA_012961055.1	s__LS-NOB sp012961055	78.7031	204	871	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:08:17,373] [INFO] GTDB search result was written to GCA_018694935.1_ASM1869493v1_genomic.fna/result_gtdb.tsv
[2023-06-19 06:08:17,373] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:08:17,377] [INFO] DFAST_QC result json was written to GCA_018694935.1_ASM1869493v1_genomic.fna/dqc_result.json
[2023-06-19 06:08:17,377] [INFO] DFAST_QC completed!
[2023-06-19 06:08:17,377] [INFO] Total running time: 0h0m58s