[2023-06-19 00:40:32,806] [INFO] DFAST_QC pipeline started.
[2023-06-19 00:40:32,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 00:40:32,808] [INFO] DQC Reference Directory: /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference
[2023-06-19 00:40:33,983] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 00:40:33,984] [INFO] Task started: Prodigal
[2023-06-19 00:40:33,984] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c2f430c-217b-42d8-a874-098d8d3701ad/GCA_018054055.1_ASM1805405v1_genomic.fna.gz | prodigal -d GCA_018054055.1_ASM1805405v1_genomic.fna/cds.fna -a GCA_018054055.1_ASM1805405v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 00:40:43,963] [INFO] Task succeeded: Prodigal
[2023-06-19 00:40:43,963] [INFO] Task started: HMMsearch
[2023-06-19 00:40:43,963] [INFO] Running command: hmmsearch --tblout GCA_018054055.1_ASM1805405v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/reference_markers.hmm GCA_018054055.1_ASM1805405v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 00:40:44,131] [INFO] Task succeeded: HMMsearch
[2023-06-19 00:40:44,133] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0c2f430c-217b-42d8-a874-098d8d3701ad/GCA_018054055.1_ASM1805405v1_genomic.fna.gz]
[2023-06-19 00:40:44,163] [INFO] Query marker FASTA was written to GCA_018054055.1_ASM1805405v1_genomic.fna/markers.fasta
[2023-06-19 00:40:44,163] [INFO] Task started: Blastn
[2023-06-19 00:40:44,164] [INFO] Running command: blastn -query GCA_018054055.1_ASM1805405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/reference_markers.fasta -out GCA_018054055.1_ASM1805405v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:40:44,750] [INFO] Task succeeded: Blastn
[2023-06-19 00:40:44,758] [INFO] Selected 22 target genomes.
[2023-06-19 00:40:44,758] [INFO] Target genome list was writen to GCA_018054055.1_ASM1805405v1_genomic.fna/target_genomes.txt
[2023-06-19 00:40:44,760] [INFO] Task started: fastANI
[2023-06-19 00:40:44,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c2f430c-217b-42d8-a874-098d8d3701ad/GCA_018054055.1_ASM1805405v1_genomic.fna.gz --refList GCA_018054055.1_ASM1805405v1_genomic.fna/target_genomes.txt --output GCA_018054055.1_ASM1805405v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 00:40:59,398] [INFO] Task succeeded: fastANI
[2023-06-19 00:40:59,399] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 00:40:59,399] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 00:40:59,413] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 00:40:59,413] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 00:40:59,414] [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
Alistipes onderdonkii	strain=DSM 19147	GCA_025145285.1	328813	328813	type	True	77.0434	64	549	95	below_threshold
Alistipes senegalensis	strain=JC50	GCA_025145645.1	1288121	1288121	type	True	76.771	77	549	95	below_threshold
Gallalistipes aquisgranensis	strain=DSM 108975	GCA_014982715.1	2779358	2779358	type	True	76.6585	86	549	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_025145845.1	328814	328814	suspected-type	True	76.6254	73	549	95	below_threshold
Alistipes communis	strain=5CBH24	GCA_006542665.1	2585118	2585118	type	True	76.6082	65	549	95	below_threshold
Alistipes megaguti	strain=Marseille-P5997	GCA_900604385.1	2364787	2364787	type	True	76.6031	75	549	95	below_threshold
Alistipes shahii	strain=WAL 8301	GCA_000210575.1	328814	328814	suspected-type	True	76.5815	76	549	95	below_threshold
Alistipes finegoldii	strain=DSM 17242	GCA_000265365.1	214856	214856	type	True	76.4682	80	549	95	below_threshold
Alistipes montrealensis	strain=kh20	GCA_018362775.1	2834113	2834113	type	True	75.8934	60	549	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 00:40:59,416] [INFO] DFAST Taxonomy check result was written to GCA_018054055.1_ASM1805405v1_genomic.fna/tc_result.tsv
[2023-06-19 00:40:59,416] [INFO] ===== Taxonomy check completed =====
[2023-06-19 00:40:59,416] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 00:40:59,417] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/checkm_data
[2023-06-19 00:40:59,418] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 00:40:59,439] [INFO] Task started: CheckM
[2023-06-19 00:40:59,440] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054055.1_ASM1805405v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054055.1_ASM1805405v1_genomic.fna/checkm_input GCA_018054055.1_ASM1805405v1_genomic.fna/checkm_result
[2023-06-19 00:41:30,130] [INFO] Task succeeded: CheckM
[2023-06-19 00:41:30,131] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 54.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 00:41:30,153] [INFO] ===== Completeness check finished =====
[2023-06-19 00:41:30,154] [INFO] ===== Start GTDB Search =====
[2023-06-19 00:41:30,154] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054055.1_ASM1805405v1_genomic.fna/markers.fasta)
[2023-06-19 00:41:30,154] [INFO] Task started: Blastn
[2023-06-19 00:41:30,154] [INFO] Running command: blastn -query GCA_018054055.1_ASM1805405v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge08f1208-183c-4731-ba85-931409691f53/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054055.1_ASM1805405v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 00:41:30,996] [INFO] Task succeeded: Blastn
[2023-06-19 00:41:31,005] [INFO] Selected 11 target genomes.
[2023-06-19 00:41:31,005] [INFO] Target genome list was writen to GCA_018054055.1_ASM1805405v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 00:41:31,008] [INFO] Task started: fastANI
[2023-06-19 00:41:31,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c2f430c-217b-42d8-a874-098d8d3701ad/GCA_018054055.1_ASM1805405v1_genomic.fna.gz --refList GCA_018054055.1_ASM1805405v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054055.1_ASM1805405v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 00:41:35,528] [INFO] Task succeeded: fastANI
[2023-06-19 00:41:35,535] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 00:41:35,535] [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_900104605.1	s__Tidjanibacter inops_A	99.3746	525	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	99.31	98.92	0.96	0.89	16	conclusive
GCA_019114205.1	s__Tidjanibacter gallistercoris	82.9207	410	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577285.1	s__Tidjanibacter sp910577285	82.6706	398	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116245.1	s__Tidjanibacter faecipullorum	78.7273	212	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Tidjanibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542505.1	s__Alistipes stercorigallinarum	77.1079	62	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	98.83	98.70	0.90	0.85	3	-
GCA_017935625.1	s__RGIG9113 sp017935625	77.085	92	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__RGIG9113	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014982715.1	s__DSM-108975 sp014982715	76.6585	86	549	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__DSM-108975	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 00:41:35,537] [INFO] GTDB search result was written to GCA_018054055.1_ASM1805405v1_genomic.fna/result_gtdb.tsv
[2023-06-19 00:41:35,537] [INFO] ===== GTDB Search completed =====
[2023-06-19 00:41:35,542] [INFO] DFAST_QC result json was written to GCA_018054055.1_ASM1805405v1_genomic.fna/dqc_result.json
[2023-06-19 00:41:35,542] [INFO] DFAST_QC completed!
[2023-06-19 00:41:35,542] [INFO] Total running time: 0h1m3s