[2023-06-18 13:18:55,150] [INFO] DFAST_QC pipeline started.
[2023-06-18 13:18:55,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 13:18:55,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference
[2023-06-18 13:18:56,500] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 13:18:56,501] [INFO] Task started: Prodigal
[2023-06-18 13:18:56,502] [INFO] Running command: gunzip -c /var/lib/cwl/stgf6c62a09-fa2e-4e49-98a3-fee4ff09194c/GCA_018052765.1_ASM1805276v1_genomic.fna.gz | prodigal -d GCA_018052765.1_ASM1805276v1_genomic.fna/cds.fna -a GCA_018052765.1_ASM1805276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 13:19:03,725] [INFO] Task succeeded: Prodigal
[2023-06-18 13:19:03,725] [INFO] Task started: HMMsearch
[2023-06-18 13:19:03,725] [INFO] Running command: hmmsearch --tblout GCA_018052765.1_ASM1805276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/reference_markers.hmm GCA_018052765.1_ASM1805276v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 13:19:03,979] [INFO] Task succeeded: HMMsearch
[2023-06-18 13:19:03,983] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf6c62a09-fa2e-4e49-98a3-fee4ff09194c/GCA_018052765.1_ASM1805276v1_genomic.fna.gz]
[2023-06-18 13:19:04,015] [INFO] Query marker FASTA was written to GCA_018052765.1_ASM1805276v1_genomic.fna/markers.fasta
[2023-06-18 13:19:04,015] [INFO] Task started: Blastn
[2023-06-18 13:19:04,016] [INFO] Running command: blastn -query GCA_018052765.1_ASM1805276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/reference_markers.fasta -out GCA_018052765.1_ASM1805276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:04,590] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:04,594] [INFO] Selected 13 target genomes.
[2023-06-18 13:19:04,594] [INFO] Target genome list was writen to GCA_018052765.1_ASM1805276v1_genomic.fna/target_genomes.txt
[2023-06-18 13:19:04,597] [INFO] Task started: fastANI
[2023-06-18 13:19:04,597] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c62a09-fa2e-4e49-98a3-fee4ff09194c/GCA_018052765.1_ASM1805276v1_genomic.fna.gz --refList GCA_018052765.1_ASM1805276v1_genomic.fna/target_genomes.txt --output GCA_018052765.1_ASM1805276v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 13:19:11,481] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:11,482] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 13:19:11,482] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 13:19:11,484] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 13:19:11,484] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 13:19:11,484] [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
--------------------------------------------------------------------------------
[2023-06-18 13:19:11,489] [INFO] DFAST Taxonomy check result was written to GCA_018052765.1_ASM1805276v1_genomic.fna/tc_result.tsv
[2023-06-18 13:19:11,492] [INFO] ===== Taxonomy check completed =====
[2023-06-18 13:19:11,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 13:19:11,493] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/checkm_data
[2023-06-18 13:19:11,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 13:19:11,523] [INFO] Task started: CheckM
[2023-06-18 13:19:11,523] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018052765.1_ASM1805276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018052765.1_ASM1805276v1_genomic.fna/checkm_input GCA_018052765.1_ASM1805276v1_genomic.fna/checkm_result
[2023-06-18 13:19:38,786] [INFO] Task succeeded: CheckM
[2023-06-18 13:19:38,787] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 13:19:38,820] [INFO] ===== Completeness check finished =====
[2023-06-18 13:19:38,821] [INFO] ===== Start GTDB Search =====
[2023-06-18 13:19:38,821] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018052765.1_ASM1805276v1_genomic.fna/markers.fasta)
[2023-06-18 13:19:38,822] [INFO] Task started: Blastn
[2023-06-18 13:19:38,822] [INFO] Running command: blastn -query GCA_018052765.1_ASM1805276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8ae0058-a800-421d-905a-a346717b1ad8/dqc_reference/reference_markers_gtdb.fasta -out GCA_018052765.1_ASM1805276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 13:19:39,536] [INFO] Task succeeded: Blastn
[2023-06-18 13:19:39,542] [INFO] Selected 15 target genomes.
[2023-06-18 13:19:39,542] [INFO] Target genome list was writen to GCA_018052765.1_ASM1805276v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 13:19:39,741] [INFO] Task started: fastANI
[2023-06-18 13:19:39,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgf6c62a09-fa2e-4e49-98a3-fee4ff09194c/GCA_018052765.1_ASM1805276v1_genomic.fna.gz --refList GCA_018052765.1_ASM1805276v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018052765.1_ASM1805276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 13:19:45,854] [INFO] Task succeeded: fastANI
[2023-06-18 13:19:45,878] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 13:19:45,878] [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_002340405.1	s__UBA1179 sp002340405	98.2652	381	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.50	98.24	0.87	0.80	7	conclusive
GCA_900318995.1	s__UBA1179 sp900318995	77.9772	128	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.89	96.18	0.89	0.85	8	-
GCA_017557635.1	s__UBA1179 sp017557635	77.8522	134	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.04	96.04	0.85	0.85	2	-
GCA_017633615.1	s__UBA1179 sp017633615	77.7544	109	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551845.1	s__UBA1179 sp017551845	77.6773	130	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551925.1	s__UBA1179 sp017551925	77.6182	118	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902763885.1	s__UBA1179 sp902763885	77.5883	111	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017530735.1	s__UBA1179 sp017530735	77.5273	116	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.35	98.35	0.83	0.83	2	-
GCA_905234745.1	s__UBA1179 sp905234745	77.4563	123	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017642425.1	s__UBA1179 sp017642425	77.4361	125	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651315.1	s__UBA1179 sp017651315	77.3166	144	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.72	97.72	0.81	0.81	2	-
GCA_902760965.1	s__UBA1179 sp902760965	77.1811	114	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.44	97.44	0.87	0.87	2	-
GCA_902799685.1	s__UBA1179 sp902799685	76.9992	117	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.39	96.39	0.82	0.82	2	-
GCA_002310175.1	s__UBA1179 sp002310175	76.9587	110	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774275.1	s__UBA1179 sp902774275	76.7869	107	479	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 13:19:45,883] [INFO] GTDB search result was written to GCA_018052765.1_ASM1805276v1_genomic.fna/result_gtdb.tsv
[2023-06-18 13:19:45,884] [INFO] ===== GTDB Search completed =====
[2023-06-18 13:19:45,889] [INFO] DFAST_QC result json was written to GCA_018052765.1_ASM1805276v1_genomic.fna/dqc_result.json
[2023-06-18 13:19:45,890] [INFO] DFAST_QC completed!
[2023-06-18 13:19:45,890] [INFO] Total running time: 0h0m51s