[2023-06-30 13:47:15,704] [INFO] DFAST_QC pipeline started.
[2023-06-30 13:47:15,706] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 13:47:15,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference
[2023-06-30 13:47:17,124] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 13:47:17,125] [INFO] Task started: Prodigal
[2023-06-30 13:47:17,125] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfb9f71b-7e59-42ec-83bf-59266f9a9926/GCA_016708935.1_ASM1670893v1_genomic.fna.gz | prodigal -d GCA_016708935.1_ASM1670893v1_genomic.fna/cds.fna -a GCA_016708935.1_ASM1670893v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 13:47:39,108] [INFO] Task succeeded: Prodigal
[2023-06-30 13:47:39,108] [INFO] Task started: HMMsearch
[2023-06-30 13:47:39,109] [INFO] Running command: hmmsearch --tblout GCA_016708935.1_ASM1670893v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/reference_markers.hmm GCA_016708935.1_ASM1670893v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 13:47:39,423] [INFO] Task succeeded: HMMsearch
[2023-06-30 13:47:39,424] [INFO] Found 6/6 markers.
[2023-06-30 13:47:39,471] [INFO] Query marker FASTA was written to GCA_016708935.1_ASM1670893v1_genomic.fna/markers.fasta
[2023-06-30 13:47:39,472] [INFO] Task started: Blastn
[2023-06-30 13:47:39,472] [INFO] Running command: blastn -query GCA_016708935.1_ASM1670893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/reference_markers.fasta -out GCA_016708935.1_ASM1670893v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:47:40,056] [INFO] Task succeeded: Blastn
[2023-06-30 13:47:40,061] [INFO] Selected 27 target genomes.
[2023-06-30 13:47:40,061] [INFO] Target genome list was writen to GCA_016708935.1_ASM1670893v1_genomic.fna/target_genomes.txt
[2023-06-30 13:47:40,069] [INFO] Task started: fastANI
[2023-06-30 13:47:40,069] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb9f71b-7e59-42ec-83bf-59266f9a9926/GCA_016708935.1_ASM1670893v1_genomic.fna.gz --refList GCA_016708935.1_ASM1670893v1_genomic.fna/target_genomes.txt --output GCA_016708935.1_ASM1670893v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 13:48:01,204] [INFO] Task succeeded: fastANI
[2023-06-30 13:48:01,205] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 13:48:01,206] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 13:48:01,214] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 13:48:01,214] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 13:48:01,215] [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
Leadbetterella byssophila	strain=DSM 17132	GCA_000166395.1	316068	316068	type	True	77.8464	76	1733	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	77.5139	248	1733	95	below_threshold
Marinilongibacter aquaticus	strain=YYF0007	GCA_020149935.1	2975157	2975157	type	True	76.822	52	1733	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_004329705.1	1605367	1605367	type	True	76.4143	50	1733	95	below_threshold
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	76.0594	93	1733	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	75.8977	63	1733	95	below_threshold
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	75.4898	80	1733	95	below_threshold
Flavobacterium psychroterrae	strain=CCM 8827	GCA_018380615.1	2133767	2133767	type	True	74.8527	50	1733	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 13:48:01,217] [INFO] DFAST Taxonomy check result was written to GCA_016708935.1_ASM1670893v1_genomic.fna/tc_result.tsv
[2023-06-30 13:48:01,218] [INFO] ===== Taxonomy check completed =====
[2023-06-30 13:48:01,218] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 13:48:01,218] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/checkm_data
[2023-06-30 13:48:01,220] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 13:48:01,272] [INFO] Task started: CheckM
[2023-06-30 13:48:01,272] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708935.1_ASM1670893v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708935.1_ASM1670893v1_genomic.fna/checkm_input GCA_016708935.1_ASM1670893v1_genomic.fna/checkm_result
[2023-06-30 13:49:04,468] [INFO] Task succeeded: CheckM
[2023-06-30 13:49:04,470] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 13:49:04,494] [INFO] ===== Completeness check finished =====
[2023-06-30 13:49:04,494] [INFO] ===== Start GTDB Search =====
[2023-06-30 13:49:04,495] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708935.1_ASM1670893v1_genomic.fna/markers.fasta)
[2023-06-30 13:49:04,495] [INFO] Task started: Blastn
[2023-06-30 13:49:04,495] [INFO] Running command: blastn -query GCA_016708935.1_ASM1670893v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg50c49a21-c251-403e-93bc-16bef79bb00c/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708935.1_ASM1670893v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 13:49:05,228] [INFO] Task succeeded: Blastn
[2023-06-30 13:49:05,234] [INFO] Selected 28 target genomes.
[2023-06-30 13:49:05,234] [INFO] Target genome list was writen to GCA_016708935.1_ASM1670893v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 13:49:05,252] [INFO] Task started: fastANI
[2023-06-30 13:49:05,253] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfb9f71b-7e59-42ec-83bf-59266f9a9926/GCA_016708935.1_ASM1670893v1_genomic.fna.gz --refList GCA_016708935.1_ASM1670893v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708935.1_ASM1670893v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 13:49:25,757] [INFO] Task succeeded: fastANI
[2023-06-30 13:49:25,771] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 13:49:25,771] [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_016722655.1	s__Leadbetterella sp016722655	99.0722	1557	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	99.38	99.07	0.96	0.94	5	conclusive
GCF_000166395.1	s__Leadbetterella byssophila	77.5422	74	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002256295.1	s__Leadbetterella sp002256295	77.3533	190	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCF_009905725.1	s__Leadbetterella sp002483125	76.343	107	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	98.11	98.11	0.94	0.94	2	-
GCF_002855535.1	s__Emticicia sp002855535	76.1566	50	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014644295.1	s__Emticicia aquatilis	76.0594	93	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495105.1	s__Emticicia sp017495105	75.7694	73	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005280585.1	s__Dyadobacter frigoris	75.5118	54	1733	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Dyadobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 13:49:25,773] [INFO] GTDB search result was written to GCA_016708935.1_ASM1670893v1_genomic.fna/result_gtdb.tsv
[2023-06-30 13:49:25,774] [INFO] ===== GTDB Search completed =====
[2023-06-30 13:49:25,777] [INFO] DFAST_QC result json was written to GCA_016708935.1_ASM1670893v1_genomic.fna/dqc_result.json
[2023-06-30 13:49:25,777] [INFO] DFAST_QC completed!
[2023-06-30 13:49:25,777] [INFO] Total running time: 0h2m10s