[2024-01-24 13:18:41,139] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,141] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,141] [INFO] DQC Reference Directory: /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference
[2024-01-24 13:18:42,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:42,326] [INFO] Task started: Prodigal
[2024-01-24 13:18:42,326] [INFO] Running command: gunzip -c /var/lib/cwl/stgf1e8c954-d98c-4a7f-b50a-b6948c186f35/GCF_014297335.1_ASM1429733v1_genomic.fna.gz | prodigal -d GCF_014297335.1_ASM1429733v1_genomic.fna/cds.fna -a GCF_014297335.1_ASM1429733v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:49,254] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:49,255] [INFO] Task started: HMMsearch
[2024-01-24 13:18:49,255] [INFO] Running command: hmmsearch --tblout GCF_014297335.1_ASM1429733v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/reference_markers.hmm GCF_014297335.1_ASM1429733v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:49,521] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:49,523] [INFO] Found 6/6 markers.
[2024-01-24 13:18:49,550] [INFO] Query marker FASTA was written to GCF_014297335.1_ASM1429733v1_genomic.fna/markers.fasta
[2024-01-24 13:18:49,551] [INFO] Task started: Blastn
[2024-01-24 13:18:49,551] [INFO] Running command: blastn -query GCF_014297335.1_ASM1429733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/reference_markers.fasta -out GCF_014297335.1_ASM1429733v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:50,204] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:50,207] [INFO] Selected 18 target genomes.
[2024-01-24 13:18:50,207] [INFO] Target genome list was writen to GCF_014297335.1_ASM1429733v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:50,243] [INFO] Task started: fastANI
[2024-01-24 13:18:50,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e8c954-d98c-4a7f-b50a-b6948c186f35/GCF_014297335.1_ASM1429733v1_genomic.fna.gz --refList GCF_014297335.1_ASM1429733v1_genomic.fna/target_genomes.txt --output GCF_014297335.1_ASM1429733v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:59,220] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:59,221] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:59,221] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:59,237] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:18:59,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:18:59,237] [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
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.3108	91	892	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.2139	94	892	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	80.6063	89	892	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.4271	233	892	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.3922	230	892	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.3421	228	892	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	79.0724	204	892	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.5905	177	892	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.5591	148	892	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.4474	106	892	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.1251	74	892	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.0303	103	892	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	77.9296	147	892	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.8549	77	892	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.6517	56	892	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.3979	114	892	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:59,239] [INFO] DFAST Taxonomy check result was written to GCF_014297335.1_ASM1429733v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:59,239] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:59,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:59,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/checkm_data
[2024-01-24 13:18:59,241] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:59,268] [INFO] Task started: CheckM
[2024-01-24 13:18:59,268] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014297335.1_ASM1429733v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014297335.1_ASM1429733v1_genomic.fna/checkm_input GCF_014297335.1_ASM1429733v1_genomic.fna/checkm_result
[2024-01-24 13:19:25,659] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:25,660] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:25,686] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:25,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:25,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014297335.1_ASM1429733v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:25,687] [INFO] Task started: Blastn
[2024-01-24 13:19:25,687] [INFO] Running command: blastn -query GCF_014297335.1_ASM1429733v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86ffcd9f-1369-4514-ab30-f4ad0d3b4a78/dqc_reference/reference_markers_gtdb.fasta -out GCF_014297335.1_ASM1429733v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:26,823] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:26,826] [INFO] Selected 17 target genomes.
[2024-01-24 13:19:26,826] [INFO] Target genome list was writen to GCF_014297335.1_ASM1429733v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:26,952] [INFO] Task started: fastANI
[2024-01-24 13:19:26,952] [INFO] Running command: fastANI --query /var/lib/cwl/stgf1e8c954-d98c-4a7f-b50a-b6948c186f35/GCF_014297335.1_ASM1429733v1_genomic.fna.gz --refList GCF_014297335.1_ASM1429733v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014297335.1_ASM1429733v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:36,502] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:36,520] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:36,520] [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_902363825.1	s__CAG-45 sp000438375	98.9868	775	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	98.60	98.28	0.92	0.87	6	conclusive
GCA_900771955.1	s__CAG-45 sp900771955	85.5544	553	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900537995.1	s__Roseburia intestinalis	79.3309	229	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.51	98.07	0.86	0.80	21	-
GCF_000225345.1	s__Roseburia hominis	79.0747	202	892	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_003470905.1	s__Roseburia sp003470905	78.8375	209	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCA_900542495.1	s__Roseburia sp900542495	78.8369	168	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.47	97.09	0.82	0.76	4	-
GCF_003479605.1	s__RUG115 sp900066395	78.7217	159	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	98.27	97.78	0.88	0.83	29	-
GCF_000174195.1	s__Roseburia inulinivorans	78.5933	177	892	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_001406815.1	s__Agathobacter faecis	78.531	149	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCA_002299665.1	s__CAG-45 sp002299665	78.4668	180	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-45	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003483745.1	s__Roseburia sp003483745	77.9492	169	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	97.45	97.41	0.84	0.84	3	-
GCA_900315735.1	s__RUG115 sp900315735	77.8163	156	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	99.35	98.93	0.92	0.85	5	-
GCA_900550935.1	s__Roseburia sp900550935	77.683	180	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.33	98.19	0.83	0.82	3	-
GCA_902782995.1	s__RUG115 sp902782995	77.5478	157	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__RUG115	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017937095.1	s__Roseburia sp017937095	77.3689	163	892	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_900546495.1	s__Eubacterium_I sp900546495	77.2139	100	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	99.94	99.87	0.93	0.88	3	-
GCA_910586445.1	s__Eubacterium_J sp910586445	76.5393	70	892	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_J	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:36,522] [INFO] GTDB search result was written to GCF_014297335.1_ASM1429733v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:36,522] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:36,526] [INFO] DFAST_QC result json was written to GCF_014297335.1_ASM1429733v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:36,526] [INFO] DFAST_QC completed!
[2024-01-24 13:19:36,526] [INFO] Total running time: 0h0m55s