[2023-06-28 13:32:51,809] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:32:51,811] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:32:51,811] [INFO] DQC Reference Directory: /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference
[2023-06-28 13:32:53,042] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:32:53,043] [INFO] Task started: Prodigal
[2023-06-28 13:32:53,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d35657-ce3e-4249-9e80-78f1fcf30bf2/GCA_017550455.1_ASM1755045v1_genomic.fna.gz | prodigal -d GCA_017550455.1_ASM1755045v1_genomic.fna/cds.fna -a GCA_017550455.1_ASM1755045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:33:08,261] [INFO] Task succeeded: Prodigal
[2023-06-28 13:33:08,261] [INFO] Task started: HMMsearch
[2023-06-28 13:33:08,262] [INFO] Running command: hmmsearch --tblout GCA_017550455.1_ASM1755045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/reference_markers.hmm GCA_017550455.1_ASM1755045v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:33:08,517] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:33:08,519] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg86d35657-ce3e-4249-9e80-78f1fcf30bf2/GCA_017550455.1_ASM1755045v1_genomic.fna.gz]
[2023-06-28 13:33:08,553] [INFO] Query marker FASTA was written to GCA_017550455.1_ASM1755045v1_genomic.fna/markers.fasta
[2023-06-28 13:33:08,553] [INFO] Task started: Blastn
[2023-06-28 13:33:08,554] [INFO] Running command: blastn -query GCA_017550455.1_ASM1755045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/reference_markers.fasta -out GCA_017550455.1_ASM1755045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:33:09,192] [INFO] Task succeeded: Blastn
[2023-06-28 13:33:09,197] [INFO] Selected 21 target genomes.
[2023-06-28 13:33:09,197] [INFO] Target genome list was writen to GCA_017550455.1_ASM1755045v1_genomic.fna/target_genomes.txt
[2023-06-28 13:33:09,199] [INFO] Task started: fastANI
[2023-06-28 13:33:09,199] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d35657-ce3e-4249-9e80-78f1fcf30bf2/GCA_017550455.1_ASM1755045v1_genomic.fna.gz --refList GCA_017550455.1_ASM1755045v1_genomic.fna/target_genomes.txt --output GCA_017550455.1_ASM1755045v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:33:18,383] [INFO] Task succeeded: fastANI
[2023-06-28 13:33:18,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:33:18,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:33:18,393] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:33:18,393] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:33:18,393] [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 ruminicola	strain=ATCC 19189	GCA_900108375.1	839	839	type	True	76.869	83	891	95	below_threshold
Prevotella ruminicola	strain=Bryant 23	GCA_000025925.1	839	839	type	True	76.8387	84	891	95	below_threshold
Prevotella buccae	strain=ATCC 33574	GCA_000184945.1	28126	28126	type	True	76.7674	55	891	95	below_threshold
Prevotella albensis	strain=JCM 12258	GCA_000613525.1	77768	77768	type	True	76.3	50	891	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:33:18,396] [INFO] DFAST Taxonomy check result was written to GCA_017550455.1_ASM1755045v1_genomic.fna/tc_result.tsv
[2023-06-28 13:33:18,396] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:33:18,397] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:33:18,397] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/checkm_data
[2023-06-28 13:33:18,398] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:33:18,433] [INFO] Task started: CheckM
[2023-06-28 13:33:18,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017550455.1_ASM1755045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017550455.1_ASM1755045v1_genomic.fna/checkm_input GCA_017550455.1_ASM1755045v1_genomic.fna/checkm_result
[2023-06-28 13:34:06,492] [INFO] Task succeeded: CheckM
[2023-06-28 13:34:06,493] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 13:34:06,515] [INFO] ===== Completeness check finished =====
[2023-06-28 13:34:06,516] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:34:06,516] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017550455.1_ASM1755045v1_genomic.fna/markers.fasta)
[2023-06-28 13:34:06,517] [INFO] Task started: Blastn
[2023-06-28 13:34:06,517] [INFO] Running command: blastn -query GCA_017550455.1_ASM1755045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34e4f034-7331-496c-9c3e-b501e0c20e8b/dqc_reference/reference_markers_gtdb.fasta -out GCA_017550455.1_ASM1755045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:34:07,474] [INFO] Task succeeded: Blastn
[2023-06-28 13:34:07,480] [INFO] Selected 14 target genomes.
[2023-06-28 13:34:07,480] [INFO] Target genome list was writen to GCA_017550455.1_ASM1755045v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:34:07,484] [INFO] Task started: fastANI
[2023-06-28 13:34:07,484] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d35657-ce3e-4249-9e80-78f1fcf30bf2/GCA_017550455.1_ASM1755045v1_genomic.fna.gz --refList GCA_017550455.1_ASM1755045v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017550455.1_ASM1755045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:34:15,371] [INFO] Task succeeded: fastANI
[2023-06-28 13:34:15,389] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:34:15,390] [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_017550455.1	s__Prevotella sp017550455	100.0	873	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.96	96.96	0.76	0.76	2	conclusive
GCA_016291915.1	s__Prevotella sp016291915	94.7308	570	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797505.1	s__Prevotella sp902797505	81.7763	450	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.08	95.72	0.78	0.72	7	-
GCA_017561825.1	s__Prevotella sp017561825	77.6529	144	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287755.1	s__Prevotella sp016287755	77.4305	150	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316985.1	s__Prevotella sp900316985	77.3609	136	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.90	96.04	0.81	0.71	7	-
GCA_900314935.1	s__Prevotella sp900314935	77.3509	157	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.60	95.61	0.87	0.77	15	-
GCA_902768785.1	s__Prevotella sp902768785	77.3301	161	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.99	96.99	0.86	0.86	2	-
GCA_017651265.1	s__Prevotella sp017651265	77.2198	152	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	96.61	95.61	0.89	0.81	3	-
GCA_002361535.1	s__Prevotella sp002361535	76.8014	107	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788605.1	s__Prevotella sp902788605	76.468	61	891	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Prevotella	95.0	98.22	98.10	0.87	0.84	7	-
--------------------------------------------------------------------------------
[2023-06-28 13:34:15,393] [INFO] GTDB search result was written to GCA_017550455.1_ASM1755045v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:34:15,394] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:34:15,399] [INFO] DFAST_QC result json was written to GCA_017550455.1_ASM1755045v1_genomic.fna/dqc_result.json
[2023-06-28 13:34:15,399] [INFO] DFAST_QC completed!
[2023-06-28 13:34:15,399] [INFO] Total running time: 0h1m24s