[2023-06-18 10:35:27,308] [INFO] DFAST_QC pipeline started.
[2023-06-18 10:35:27,311] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 10:35:27,311] [INFO] DQC Reference Directory: /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference
[2023-06-18 10:35:28,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 10:35:28,615] [INFO] Task started: Prodigal
[2023-06-18 10:35:28,616] [INFO] Running command: gunzip -c /var/lib/cwl/stg639460c7-7118-4485-8e13-72aa6bc5ebd9/GCA_029227135.1_ASM2922713v1_genomic.fna.gz | prodigal -d GCA_029227135.1_ASM2922713v1_genomic.fna/cds.fna -a GCA_029227135.1_ASM2922713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 10:35:47,931] [INFO] Task succeeded: Prodigal
[2023-06-18 10:35:47,932] [INFO] Task started: HMMsearch
[2023-06-18 10:35:47,932] [INFO] Running command: hmmsearch --tblout GCA_029227135.1_ASM2922713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/reference_markers.hmm GCA_029227135.1_ASM2922713v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 10:35:48,190] [INFO] Task succeeded: HMMsearch
[2023-06-18 10:35:48,192] [INFO] Found 6/6 markers.
[2023-06-18 10:35:48,227] [INFO] Query marker FASTA was written to GCA_029227135.1_ASM2922713v1_genomic.fna/markers.fasta
[2023-06-18 10:35:48,228] [INFO] Task started: Blastn
[2023-06-18 10:35:48,228] [INFO] Running command: blastn -query GCA_029227135.1_ASM2922713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/reference_markers.fasta -out GCA_029227135.1_ASM2922713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:35:48,849] [INFO] Task succeeded: Blastn
[2023-06-18 10:35:48,855] [INFO] Selected 18 target genomes.
[2023-06-18 10:35:48,855] [INFO] Target genome list was writen to GCA_029227135.1_ASM2922713v1_genomic.fna/target_genomes.txt
[2023-06-18 10:35:48,859] [INFO] Task started: fastANI
[2023-06-18 10:35:48,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg639460c7-7118-4485-8e13-72aa6bc5ebd9/GCA_029227135.1_ASM2922713v1_genomic.fna.gz --refList GCA_029227135.1_ASM2922713v1_genomic.fna/target_genomes.txt --output GCA_029227135.1_ASM2922713v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 10:36:00,049] [INFO] Task succeeded: fastANI
[2023-06-18 10:36:00,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 10:36:00,051] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 10:36:00,061] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2023-06-18 10:36:00,061] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 10:36:00,061] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	98.5855	828	869	95	conclusive
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	98.5539	840	869	95	conclusive
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	76.6416	69	869	95	below_threshold
Muribaculum gordoncarteri	strain=TLL-A4	GCA_004803695.1	2530390	2530390	type	True	76.2684	50	869	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 10:36:00,067] [INFO] DFAST Taxonomy check result was written to GCA_029227135.1_ASM2922713v1_genomic.fna/tc_result.tsv
[2023-06-18 10:36:00,068] [INFO] ===== Taxonomy check completed =====
[2023-06-18 10:36:00,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 10:36:00,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/checkm_data
[2023-06-18 10:36:00,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 10:36:00,103] [INFO] Task started: CheckM
[2023-06-18 10:36:00,104] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029227135.1_ASM2922713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029227135.1_ASM2922713v1_genomic.fna/checkm_input GCA_029227135.1_ASM2922713v1_genomic.fna/checkm_result
[2023-06-18 10:36:54,550] [INFO] Task succeeded: CheckM
[2023-06-18 10:36:54,552] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 10:36:54,583] [INFO] ===== Completeness check finished =====
[2023-06-18 10:36:54,583] [INFO] ===== Start GTDB Search =====
[2023-06-18 10:36:54,584] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029227135.1_ASM2922713v1_genomic.fna/markers.fasta)
[2023-06-18 10:36:54,584] [INFO] Task started: Blastn
[2023-06-18 10:36:54,584] [INFO] Running command: blastn -query GCA_029227135.1_ASM2922713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc945733e-e6d6-4e12-80be-01d98406e134/dqc_reference/reference_markers_gtdb.fasta -out GCA_029227135.1_ASM2922713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 10:36:55,489] [INFO] Task succeeded: Blastn
[2023-06-18 10:36:55,495] [INFO] Selected 13 target genomes.
[2023-06-18 10:36:55,496] [INFO] Target genome list was writen to GCA_029227135.1_ASM2922713v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 10:36:55,505] [INFO] Task started: fastANI
[2023-06-18 10:36:55,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg639460c7-7118-4485-8e13-72aa6bc5ebd9/GCA_029227135.1_ASM2922713v1_genomic.fna.gz --refList GCA_029227135.1_ASM2922713v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029227135.1_ASM2922713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 10:37:03,495] [INFO] Task succeeded: fastANI
[2023-06-18 10:37:03,508] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 10:37:03,509] [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
GCF_009676955.1	s__Sodaliphilus pleomorphus	98.5539	840	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.46	98.06	0.93	0.87	18	conclusive
GCA_900770215.1	s__Sodaliphilus sp900770215	90.7708	744	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314215.1	s__Sodaliphilus sp900314215	84.6305	591	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	0.99	0.99	2	-
GCA_016287065.1	s__Sodaliphilus sp016287065	77.7214	157	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768435.1	s__Sodaliphilus sp902768435	77.5921	258	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065815.1	s__Sodaliphilus sp018065815	77.5566	165	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318065.1	s__Sodaliphilus sp900318065	77.5134	194	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.54	97.91	0.91	0.84	24	-
GCA_902760865.1	s__Sodaliphilus sp902760865	77.4513	196	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017619355.1	s__Sodaliphilus sp017619355	77.4443	232	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776835.1	s__Sodaliphilus sp902776835	77.4012	238	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_900318255.1	s__Sodaliphilus sp900318255	77.345	207	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.43	97.80	0.91	0.84	5	-
GCA_002476625.1	s__Sodaliphilus sp002476625	76.9751	125	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353885.1	s__Sodaliphilus sp002353885	76.9422	168	869	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.50	97.13	0.86	0.82	5	-
--------------------------------------------------------------------------------
[2023-06-18 10:37:03,513] [INFO] GTDB search result was written to GCA_029227135.1_ASM2922713v1_genomic.fna/result_gtdb.tsv
[2023-06-18 10:37:03,514] [INFO] ===== GTDB Search completed =====
[2023-06-18 10:37:03,518] [INFO] DFAST_QC result json was written to GCA_029227135.1_ASM2922713v1_genomic.fna/dqc_result.json
[2023-06-18 10:37:03,518] [INFO] DFAST_QC completed!
[2023-06-18 10:37:03,518] [INFO] Total running time: 0h1m36s