[2024-01-24 10:58:06,479] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:06,481] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:06,481] [INFO] DQC Reference Directory: /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference
[2024-01-24 10:58:09,636] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:09,637] [INFO] Task started: Prodigal
[2024-01-24 10:58:09,638] [INFO] Running command: gunzip -c /var/lib/cwl/stg3975683d-a199-4af2-8ba8-1fb4fb0d1fd3/GCF_014287435.1_ASM1428743v1_genomic.fna.gz | prodigal -d GCF_014287435.1_ASM1428743v1_genomic.fna/cds.fna -a GCF_014287435.1_ASM1428743v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:16,628] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:16,629] [INFO] Task started: HMMsearch
[2024-01-24 10:58:16,629] [INFO] Running command: hmmsearch --tblout GCF_014287435.1_ASM1428743v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/reference_markers.hmm GCF_014287435.1_ASM1428743v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:16,912] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:16,914] [INFO] Found 6/6 markers.
[2024-01-24 10:58:16,943] [INFO] Query marker FASTA was written to GCF_014287435.1_ASM1428743v1_genomic.fna/markers.fasta
[2024-01-24 10:58:16,943] [INFO] Task started: Blastn
[2024-01-24 10:58:16,943] [INFO] Running command: blastn -query GCF_014287435.1_ASM1428743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/reference_markers.fasta -out GCF_014287435.1_ASM1428743v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:17,609] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:17,612] [INFO] Selected 20 target genomes.
[2024-01-24 10:58:17,613] [INFO] Target genome list was writen to GCF_014287435.1_ASM1428743v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:17,655] [INFO] Task started: fastANI
[2024-01-24 10:58:17,655] [INFO] Running command: fastANI --query /var/lib/cwl/stg3975683d-a199-4af2-8ba8-1fb4fb0d1fd3/GCF_014287435.1_ASM1428743v1_genomic.fna.gz --refList GCF_014287435.1_ASM1428743v1_genomic.fna/target_genomes.txt --output GCF_014287435.1_ASM1428743v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:27,357] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:27,358] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:27,359] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:27,378] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:27,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:27,378] [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 lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	100.0	849	850	95	conclusive
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	80.7548	64	850	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.9271	79	850	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	79.732	70	850	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.512	122	850	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.4576	127	850	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	79.3535	126	850	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.0805	70	850	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.8099	81	850	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.6473	118	850	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	78.4849	62	850	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	78.3895	68	850	95	below_threshold
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.2569	115	850	95	below_threshold
Roseburia porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	78.2073	102	850	95	below_threshold
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	77.9047	118	850	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.859	61	850	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:27,380] [INFO] DFAST Taxonomy check result was written to GCF_014287435.1_ASM1428743v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:27,380] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:27,380] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:27,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/checkm_data
[2024-01-24 10:58:27,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:27,407] [INFO] Task started: CheckM
[2024-01-24 10:58:27,408] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287435.1_ASM1428743v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287435.1_ASM1428743v1_genomic.fna/checkm_input GCF_014287435.1_ASM1428743v1_genomic.fna/checkm_result
[2024-01-24 10:58:54,978] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:54,979] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:54,997] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:54,997] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:54,998] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287435.1_ASM1428743v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:54,998] [INFO] Task started: Blastn
[2024-01-24 10:58:54,998] [INFO] Running command: blastn -query GCF_014287435.1_ASM1428743v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge584c6ba-dd3c-4854-8c7d-5a358f749814/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287435.1_ASM1428743v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:56,144] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:56,149] [INFO] Selected 22 target genomes.
[2024-01-24 10:58:56,149] [INFO] Target genome list was writen to GCF_014287435.1_ASM1428743v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:56,172] [INFO] Task started: fastANI
[2024-01-24 10:58:56,172] [INFO] Running command: fastANI --query /var/lib/cwl/stg3975683d-a199-4af2-8ba8-1fb4fb0d1fd3/GCF_014287435.1_ASM1428743v1_genomic.fna.gz --refList GCF_014287435.1_ASM1428743v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287435.1_ASM1428743v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:59:07,711] [INFO] Task succeeded: fastANI
[2024-01-24 10:59:07,736] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:59:07,737] [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_003478275.1	s__AM51-8 sp003478275	98.9572	757	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	99.20	98.90	0.94	0.89	8	conclusive
GCA_900546435.1	s__AM51-8 sp900546435	83.1293	446	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__AM51-8	95.0	97.06	96.69	0.86	0.85	3	-
GCF_014287635.1	s__1XD42-69 sp014287635	80.133	112	850	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	-
GCF_003470905.1	s__Roseburia sp003470905	79.4873	124	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Roseburia	95.0	98.69	98.30	0.90	0.82	7	-
GCF_003479605.1	s__RUG115 sp900066395	79.4708	108	850	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_003122485.1	s__Eubacterium_I ramulus_A	79.1028	88	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eubacterium_I	95.0	98.76	98.61	0.82	0.80	7	-
GCA_902363825.1	s__CAG-45 sp000438375	78.6096	103	850	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	-
GCF_000174195.1	s__Roseburia inulinivorans	78.2569	115	850	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_013300825.1	s__Blautia_A wexlerae_B	77.9153	65	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.68	98.07	0.89	0.86	5	-
GCF_000225345.1	s__Roseburia hominis	77.8495	118	850	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_001940225.1	s__14-2 sp001940225	77.8028	72	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__14-2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315735.1	s__RUG115 sp900315735	77.6926	95	850	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_900116395.1	s__XBD2001 sp900116395	77.6236	65	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBD2001	95.0	96.26	95.68	0.91	0.86	9	-
GCA_902782995.1	s__RUG115 sp902782995	77.3777	85	850	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_015057115.1	s__XBB1006 sp015057115	77.324	52	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__XBB1006	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900543445.1	s__Agathobacter sp900543445	77.2794	76	850	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.64	98.60	0.88	0.84	3	-
GCA_017937095.1	s__Roseburia sp017937095	77.0721	66	850	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_002299665.1	s__CAG-45 sp002299665	76.7348	64	850	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	-
--------------------------------------------------------------------------------
[2024-01-24 10:59:07,739] [INFO] GTDB search result was written to GCF_014287435.1_ASM1428743v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:59:07,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:59:07,748] [INFO] DFAST_QC result json was written to GCF_014287435.1_ASM1428743v1_genomic.fna/dqc_result.json
[2024-01-24 10:59:07,748] [INFO] DFAST_QC completed!
[2024-01-24 10:59:07,748] [INFO] Total running time: 0h1m1s