[2024-01-25 20:19:05,714] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:05,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:05,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference
[2024-01-25 20:19:06,853] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:06,855] [INFO] Task started: Prodigal
[2024-01-25 20:19:06,855] [INFO] Running command: gunzip -c /var/lib/cwl/stg87419442-198d-4773-aac8-5f79bb5b0027/GCF_028539415.1_ASM2853941v1_genomic.fna.gz | prodigal -d GCF_028539415.1_ASM2853941v1_genomic.fna/cds.fna -a GCF_028539415.1_ASM2853941v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:34,345] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:34,345] [INFO] Task started: HMMsearch
[2024-01-25 20:19:34,345] [INFO] Running command: hmmsearch --tblout GCF_028539415.1_ASM2853941v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/reference_markers.hmm GCF_028539415.1_ASM2853941v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:34,680] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:34,681] [INFO] Found 6/6 markers.
[2024-01-25 20:19:34,732] [INFO] Query marker FASTA was written to GCF_028539415.1_ASM2853941v1_genomic.fna/markers.fasta
[2024-01-25 20:19:34,732] [INFO] Task started: Blastn
[2024-01-25 20:19:34,732] [INFO] Running command: blastn -query GCF_028539415.1_ASM2853941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/reference_markers.fasta -out GCF_028539415.1_ASM2853941v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:35,323] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:35,326] [INFO] Selected 12 target genomes.
[2024-01-25 20:19:35,326] [INFO] Target genome list was writen to GCF_028539415.1_ASM2853941v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:35,338] [INFO] Task started: fastANI
[2024-01-25 20:19:35,338] [INFO] Running command: fastANI --query /var/lib/cwl/stg87419442-198d-4773-aac8-5f79bb5b0027/GCF_028539415.1_ASM2853941v1_genomic.fna.gz --refList GCF_028539415.1_ASM2853941v1_genomic.fna/target_genomes.txt --output GCF_028539415.1_ASM2853941v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:49,391] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:49,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:49,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:49,402] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:19:49,402] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:19:49,402] [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
Bacteroides cellulosilyticus	strain=DSM 14838	GCA_000158035.1	246787	246787	type	True	99.8728	2204	2217	95	conclusive
Bacteroides timonensis		GCA_000513195.1	1470345	1470345	type	True	94.4171	1438	2217	95	below_threshold
Bacteroides intestinalis	strain=DSM 17393	GCA_000172175.1	329854	329854	type	True	88.6206	1302	2217	95	below_threshold
Bacteroides stercorirosoris	strain=DSM 26884	GCA_900142015.1	871324	871324	type	True	84.3148	1254	2217	95	below_threshold
Bacteroides stercorirosoris	strain=JCM 17103	GCA_000614165.1	871324	871324	type	True	84.2684	1218	2217	95	below_threshold
Bacteroides oleiciplenus	strain=YIT 12058	GCA_000315485.1	626931	626931	type	True	83.4352	1254	2217	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_000195615.1	626929	626929	type	True	79.1629	455	2217	95	below_threshold
Bacteroides clarus	strain=YIT 12056	GCA_900129655.1	626929	626929	type	True	79.1328	456	2217	95	below_threshold
Bacteroides muris	strain=KH365_2	GCA_024704915.1	2937417	2937417	type	True	79.0923	431	2217	95	below_threshold
Bacteroides uniformis	strain=ATCC 8492	GCA_025147485.1	820	820	type	True	79.0876	502	2217	95	below_threshold
Bacteroides eggerthii	strain=DSM 20697	GCA_025146565.1	28111	28111	type	True	78.9019	424	2217	95	below_threshold
Bacteroides ovatus	strain=FDAARGOS_1516	GCA_020149745.1	28116	28116	suspected-type	True	78.1539	402	2217	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:49,405] [INFO] DFAST Taxonomy check result was written to GCF_028539415.1_ASM2853941v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:49,406] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:49,406] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:49,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/checkm_data
[2024-01-25 20:19:49,407] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:49,471] [INFO] Task started: CheckM
[2024-01-25 20:19:49,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028539415.1_ASM2853941v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028539415.1_ASM2853941v1_genomic.fna/checkm_input GCF_028539415.1_ASM2853941v1_genomic.fna/checkm_result
[2024-01-25 20:21:02,955] [INFO] Task succeeded: CheckM
[2024-01-25 20:21:02,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:21:02,976] [INFO] ===== Completeness check finished =====
[2024-01-25 20:21:02,976] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:21:02,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028539415.1_ASM2853941v1_genomic.fna/markers.fasta)
[2024-01-25 20:21:02,977] [INFO] Task started: Blastn
[2024-01-25 20:21:02,977] [INFO] Running command: blastn -query GCF_028539415.1_ASM2853941v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2c1c9a37-ca5f-42c7-ac7d-92a35a10b17a/dqc_reference/reference_markers_gtdb.fasta -out GCF_028539415.1_ASM2853941v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:21:03,848] [INFO] Task succeeded: Blastn
[2024-01-25 20:21:03,851] [INFO] Selected 10 target genomes.
[2024-01-25 20:21:03,851] [INFO] Target genome list was writen to GCF_028539415.1_ASM2853941v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:21:03,863] [INFO] Task started: fastANI
[2024-01-25 20:21:03,863] [INFO] Running command: fastANI --query /var/lib/cwl/stg87419442-198d-4773-aac8-5f79bb5b0027/GCF_028539415.1_ASM2853941v1_genomic.fna.gz --refList GCF_028539415.1_ASM2853941v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028539415.1_ASM2853941v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:21:17,951] [INFO] Task succeeded: fastANI
[2024-01-25 20:21:17,958] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:21:17,958] [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_000158035.1	s__Bacteroides cellulosilyticus	99.8728	2204	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.21	95.02	0.83	0.72	42	conclusive
GCF_000513195.1	s__Bacteroides timonensis	94.4171	1438	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019129285.1	s__Bacteroides sp900552405	93.8833	1542	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.09	95.34	0.92	0.76	12	-
GCF_003464595.1	s__Bacteroides intestinalis_A	89.8063	1378	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	97.86	96.66	0.85	0.74	7	-
GCF_902364365.1	s__Bacteroides sp900556215	89.5215	1373	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.2143	99.84	99.69	0.91	0.82	3	-
GCF_000172175.1	s__Bacteroides intestinalis	88.6227	1301	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	98.18	96.30	0.86	0.76	22	-
GCA_905207245.1	s__Bacteroides sp905207245	84.3432	1092	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315485.1	s__Bacteroides oleiciplenus	83.4363	1253	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	99.39	98.79	0.93	0.86	3	-
GCA_905215555.1	s__Bacteroides sp905215555	82.9333	1001	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585845.1	s__Bacteroides sp910585845	79.6886	549	2217	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:21:17,959] [INFO] GTDB search result was written to GCF_028539415.1_ASM2853941v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:21:17,960] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:21:17,963] [INFO] DFAST_QC result json was written to GCF_028539415.1_ASM2853941v1_genomic.fna/dqc_result.json
[2024-01-25 20:21:17,963] [INFO] DFAST_QC completed!
[2024-01-25 20:21:17,963] [INFO] Total running time: 0h2m12s