[2023-06-29 20:05:50,272] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:05:50,275] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:05:50,275] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference
[2023-06-29 20:05:51,512] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:05:51,513] [INFO] Task started: Prodigal
[2023-06-29 20:05:51,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg98ede4ea-cbde-445e-a4cf-b99bdbe0914f/GCA_021628905.1_ASM2162890v1_genomic.fna.gz | prodigal -d GCA_021628905.1_ASM2162890v1_genomic.fna/cds.fna -a GCA_021628905.1_ASM2162890v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:06:07,507] [INFO] Task succeeded: Prodigal
[2023-06-29 20:06:07,508] [INFO] Task started: HMMsearch
[2023-06-29 20:06:07,508] [INFO] Running command: hmmsearch --tblout GCA_021628905.1_ASM2162890v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/reference_markers.hmm GCA_021628905.1_ASM2162890v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:06:07,793] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:06:07,794] [INFO] Found 6/6 markers.
[2023-06-29 20:06:07,843] [INFO] Query marker FASTA was written to GCA_021628905.1_ASM2162890v1_genomic.fna/markers.fasta
[2023-06-29 20:06:07,844] [INFO] Task started: Blastn
[2023-06-29 20:06:07,844] [INFO] Running command: blastn -query GCA_021628905.1_ASM2162890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/reference_markers.fasta -out GCA_021628905.1_ASM2162890v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:06:08,528] [INFO] Task succeeded: Blastn
[2023-06-29 20:06:08,533] [INFO] Selected 15 target genomes.
[2023-06-29 20:06:08,534] [INFO] Target genome list was writen to GCA_021628905.1_ASM2162890v1_genomic.fna/target_genomes.txt
[2023-06-29 20:06:08,535] [INFO] Task started: fastANI
[2023-06-29 20:06:08,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ede4ea-cbde-445e-a4cf-b99bdbe0914f/GCA_021628905.1_ASM2162890v1_genomic.fna.gz --refList GCA_021628905.1_ASM2162890v1_genomic.fna/target_genomes.txt --output GCA_021628905.1_ASM2162890v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:06:17,182] [INFO] Task succeeded: fastANI
[2023-06-29 20:06:17,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:06:17,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:06:17,194] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:06:17,194] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:06:17,194] [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
Prevotella copri	strain=DSM 18205	GCA_009495405.1	165179	165179	suspected-type	True	87.1316	579	948	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_000157935.1	165179	165179	suspected-type	True	87.0524	609	948	95	below_threshold
Prevotella copri	strain=DSM 18205	GCA_025151535.1	165179	165179	suspected-type	True	86.9715	601	948	95	below_threshold
Prevotella hominis	strain=BCRC 81118	GCA_004535825.1	2518605	2518605	type	True	84.2119	480	948	95	below_threshold
Prevotella stercorea	strain=DSM 18206	GCA_000235885.1	363265	363265	suspected-type	True	78.6602	122	948	95	below_threshold
Prevotella bryantii	strain=B14	GCA_022024235.1	77095	77095	type	True	78.011	95	948	95	below_threshold
Prevotella dentalis	strain=DSM 3688	GCA_000242335.3	52227	52227	type	True	77.9689	65	948	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	77.6935	117	948	95	below_threshold
Prevotella denticola	strain=NCTC13067	GCA_900454835.1	28129	28129	type	True	77.2368	81	948	95	below_threshold
Prevotella denticola	strain=DSM 20614	GCA_000421205.1	28129	28129	type	True	77.1959	80	948	95	below_threshold
Prevotella multiformis	strain=DSM 16608	GCA_000191065.1	282402	282402	type	True	77.0605	78	948	95	below_threshold
Prevotella illustrans	strain=A2931	GCA_017426725.1	2800387	2800387	type	True	76.9655	70	948	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:06:17,197] [INFO] DFAST Taxonomy check result was written to GCA_021628905.1_ASM2162890v1_genomic.fna/tc_result.tsv
[2023-06-29 20:06:17,198] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:06:17,198] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:06:17,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/checkm_data
[2023-06-29 20:06:17,200] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:06:17,240] [INFO] Task started: CheckM
[2023-06-29 20:06:17,240] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021628905.1_ASM2162890v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021628905.1_ASM2162890v1_genomic.fna/checkm_input GCA_021628905.1_ASM2162890v1_genomic.fna/checkm_result
[2023-06-29 20:07:06,926] [INFO] Task succeeded: CheckM
[2023-06-29 20:07:06,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:07:06,953] [INFO] ===== Completeness check finished =====
[2023-06-29 20:07:06,954] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:07:06,954] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021628905.1_ASM2162890v1_genomic.fna/markers.fasta)
[2023-06-29 20:07:06,955] [INFO] Task started: Blastn
[2023-06-29 20:07:06,955] [INFO] Running command: blastn -query GCA_021628905.1_ASM2162890v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1255a9c-5f79-4c30-896c-a681988e757a/dqc_reference/reference_markers_gtdb.fasta -out GCA_021628905.1_ASM2162890v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:07:07,818] [INFO] Task succeeded: Blastn
[2023-06-29 20:07:07,824] [INFO] Selected 12 target genomes.
[2023-06-29 20:07:07,824] [INFO] Target genome list was writen to GCA_021628905.1_ASM2162890v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:07:07,827] [INFO] Task started: fastANI
[2023-06-29 20:07:07,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg98ede4ea-cbde-445e-a4cf-b99bdbe0914f/GCA_021628905.1_ASM2162890v1_genomic.fna.gz --refList GCA_021628905.1_ASM2162890v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021628905.1_ASM2162890v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:07:15,680] [INFO] Task succeeded: fastANI
[2023-06-29 20:07:15,695] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:07:15,696] [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_900556795.1	s__Prevotella sp900556795	96.0926	396	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.39	96.16	0.81	0.77	3	conclusive
GCF_009494395.1	s__Prevotella sp900546535	94.2532	733	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.78	96.11	0.82	0.79	8	-
GCA_900770515.1	s__Prevotella sp900770515	91.633	339	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002224675.1	s__Prevotella copri_A	88.5338	631	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.28	96.07	0.78	0.74	13	-
GCA_019249655.1	s__Prevotella sp900767615	88.1405	636	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.47	95.77	0.82	0.75	7	-
GCF_019127135.1	s__Prevotella sp900551275	87.8743	636	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0063	98.12	96.96	0.86	0.77	7	-
GCA_900544825.1	s__Prevotella sp900544825	87.6781	615	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.36	98.76	0.90	0.84	3	-
GCA_900551985.1	s__Prevotella sp900551985	87.643	555	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	99.28	99.28	0.87	0.87	2	-
GCF_015074785.1	s__Prevotella sp015074785	87.4323	648	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.50	95.88	0.80	0.71	45	-
GCF_000157935.1	s__Prevotella copri	87.1029	606	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.6733	96.34	95.85	0.75	0.69	97	-
GCA_900557035.1	s__Prevotella sp900557035	86.4683	401	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	97.84	97.17	0.78	0.68	3	-
GCA_900765465.1	s__Prevotella sp900765465	84.8097	289	948	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 20:07:15,697] [INFO] GTDB search result was written to GCA_021628905.1_ASM2162890v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:07:15,698] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:07:15,702] [INFO] DFAST_QC result json was written to GCA_021628905.1_ASM2162890v1_genomic.fna/dqc_result.json
[2023-06-29 20:07:15,702] [INFO] DFAST_QC completed!
[2023-06-29 20:07:15,702] [INFO] Total running time: 0h1m25s