[2024-01-24 13:37:05,165] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:37:05,167] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:37:05,168] [INFO] DQC Reference Directory: /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference
[2024-01-24 13:37:06,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:06,545] [INFO] Task started: Prodigal
[2024-01-24 13:37:06,546] [INFO] Running command: gunzip -c /var/lib/cwl/stg7022b0c9-d3e5-4032-a428-7fa5fb7c91a4/GCF_014287515.2_ASM1428751v2_genomic.fna.gz | prodigal -d GCF_014287515.2_ASM1428751v2_genomic.fna/cds.fna -a GCF_014287515.2_ASM1428751v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:16,907] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:16,908] [INFO] Task started: HMMsearch
[2024-01-24 13:37:16,908] [INFO] Running command: hmmsearch --tblout GCF_014287515.2_ASM1428751v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/reference_markers.hmm GCF_014287515.2_ASM1428751v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:17,282] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:17,284] [INFO] Found 6/6 markers.
[2024-01-24 13:37:17,331] [INFO] Query marker FASTA was written to GCF_014287515.2_ASM1428751v2_genomic.fna/markers.fasta
[2024-01-24 13:37:17,332] [INFO] Task started: Blastn
[2024-01-24 13:37:17,332] [INFO] Running command: blastn -query GCF_014287515.2_ASM1428751v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/reference_markers.fasta -out GCF_014287515.2_ASM1428751v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:18,049] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:18,053] [INFO] Selected 13 target genomes.
[2024-01-24 13:37:18,053] [INFO] Target genome list was writen to GCF_014287515.2_ASM1428751v2_genomic.fna/target_genomes.txt
[2024-01-24 13:37:18,057] [INFO] Task started: fastANI
[2024-01-24 13:37:18,058] [INFO] Running command: fastANI --query /var/lib/cwl/stg7022b0c9-d3e5-4032-a428-7fa5fb7c91a4/GCF_014287515.2_ASM1428751v2_genomic.fna.gz --refList GCF_014287515.2_ASM1428751v2_genomic.fna/target_genomes.txt --output GCF_014287515.2_ASM1428751v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:27,523] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:27,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:27,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:27,535] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:37:27,535] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:37:27,535] [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
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	91.0607	1010	1319	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	91.0347	993	1319	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	91.0153	1023	1319	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	80.5636	356	1319	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_025147655.1	1322	1322	type	True	79.7095	84	1319	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	79.674	337	1319	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.127	102	1319	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	78.8799	104	1319	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.843	132	1319	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.7004	104	1319	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.604	222	1319	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.2893	156	1319	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.7562	75	1319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:27,537] [INFO] DFAST Taxonomy check result was written to GCF_014287515.2_ASM1428751v2_genomic.fna/tc_result.tsv
[2024-01-24 13:37:27,538] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:27,538] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:27,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/checkm_data
[2024-01-24 13:37:27,539] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:27,582] [INFO] Task started: CheckM
[2024-01-24 13:37:27,583] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287515.2_ASM1428751v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287515.2_ASM1428751v2_genomic.fna/checkm_input GCF_014287515.2_ASM1428751v2_genomic.fna/checkm_result
[2024-01-24 13:38:03,533] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:03,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:03,554] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:03,555] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:03,555] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287515.2_ASM1428751v2_genomic.fna/markers.fasta)
[2024-01-24 13:38:03,556] [INFO] Task started: Blastn
[2024-01-24 13:38:03,556] [INFO] Running command: blastn -query GCF_014287515.2_ASM1428751v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbaf25f69-8a81-4ff3-903c-bd463bb437f5/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287515.2_ASM1428751v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:04,699] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:04,703] [INFO] Selected 10 target genomes.
[2024-01-24 13:38:04,703] [INFO] Target genome list was writen to GCF_014287515.2_ASM1428751v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:04,729] [INFO] Task started: fastANI
[2024-01-24 13:38:04,729] [INFO] Running command: fastANI --query /var/lib/cwl/stg7022b0c9-d3e5-4032-a428-7fa5fb7c91a4/GCF_014287515.2_ASM1428751v2_genomic.fna.gz --refList GCF_014287515.2_ASM1428751v2_genomic.fna/target_genomes_gtdb.txt --output GCF_014287515.2_ASM1428751v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:12,807] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:12,816] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:12,816] [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_003470905.1	s__Roseburia sp003470905	98.3694	1110	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	conclusive
GCF_900537995.1	s__Roseburia intestinalis	91.0177	1022	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCA_003483745.1	s__Roseburia sp003483745	89.2996	812	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCF_000174195.1	s__Roseburia inulinivorans	80.529	358	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	95.90	0.77	0.61	28	-
GCF_014287635.1	s__1XD42-69 sp014287635	80.1309	268	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__1XD42-69	95.0	98.20	98.20	0.93	0.93	2	-
GCA_900550935.1	s__Roseburia sp900550935	79.7534	407	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCF_000225345.1	s__Roseburia hominis	79.6267	336	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.94	95.20	0.88	0.81	15	-
GCF_009695765.1	s__VUNI01 sp009695765	78.5822	226	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940165.1	s__Roseburia sp001940165	78.5733	281	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626625.1	s__Roseburia sp017626625	77.8205	170	1319	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:12,818] [INFO] GTDB search result was written to GCF_014287515.2_ASM1428751v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:12,818] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:12,822] [INFO] DFAST_QC result json was written to GCF_014287515.2_ASM1428751v2_genomic.fna/dqc_result.json
[2024-01-24 13:38:12,822] [INFO] DFAST_QC completed!
[2024-01-24 13:38:12,822] [INFO] Total running time: 0h1m8s