[2024-01-24 13:56:27,564] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:56:27,566] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:56:27,566] [INFO] DQC Reference Directory: /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference
[2024-01-24 13:56:28,915] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:56:28,916] [INFO] Task started: Prodigal
[2024-01-24 13:56:28,917] [INFO] Running command: gunzip -c /var/lib/cwl/stgf925455f-3fd3-4f90-9d11-30de418afcbb/GCF_009695765.1_ASM969576v1_genomic.fna.gz | prodigal -d GCF_009695765.1_ASM969576v1_genomic.fna/cds.fna -a GCF_009695765.1_ASM969576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:56:36,116] [INFO] Task succeeded: Prodigal
[2024-01-24 13:56:36,117] [INFO] Task started: HMMsearch
[2024-01-24 13:56:36,117] [INFO] Running command: hmmsearch --tblout GCF_009695765.1_ASM969576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/reference_markers.hmm GCF_009695765.1_ASM969576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:56:36,386] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:56:36,388] [INFO] Found 6/6 markers.
[2024-01-24 13:56:36,416] [INFO] Query marker FASTA was written to GCF_009695765.1_ASM969576v1_genomic.fna/markers.fasta
[2024-01-24 13:56:36,416] [INFO] Task started: Blastn
[2024-01-24 13:56:36,416] [INFO] Running command: blastn -query GCF_009695765.1_ASM969576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/reference_markers.fasta -out GCF_009695765.1_ASM969576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:37,058] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:37,061] [INFO] Selected 19 target genomes.
[2024-01-24 13:56:37,062] [INFO] Target genome list was writen to GCF_009695765.1_ASM969576v1_genomic.fna/target_genomes.txt
[2024-01-24 13:56:37,099] [INFO] Task started: fastANI
[2024-01-24 13:56:37,099] [INFO] Running command: fastANI --query /var/lib/cwl/stgf925455f-3fd3-4f90-9d11-30de418afcbb/GCF_009695765.1_ASM969576v1_genomic.fna.gz --refList GCF_009695765.1_ASM969576v1_genomic.fna/target_genomes.txt --output GCF_009695765.1_ASM969576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:56:46,390] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:46,391] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:56:46,391] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:56:46,409] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:56:46,410] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:56:46,410] [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 porci	strain=MUC/MUC-530-WT-4D	GCA_009695765.1	2605790	2605790	type	True	100.0	962	965	95	conclusive
Roseburia inulinivorans	strain=DSM 16841	GCA_000174195.1	360807	360807	suspected-type	True	78.8461	214	965	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.7974	238	965	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	78.7135	216	965	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	78.7132	213	965	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	78.6199	208	965	95	below_threshold
Roseburia lenta	strain=NSJ-9	GCA_014287435.1	2763061	2763061	type	True	78.5998	94	965	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	78.0226	70	965	95	below_threshold
Eubacterium ventriosum	strain=ATCC 27560	GCA_025150745.1	39496	39496	suspected-type	True	78.0132	57	965	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	77.9816	114	965	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	77.7697	76	965	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.746	69	965	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	77.7217	98	965	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.7014	71	965	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.4764	69	965	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	77.2548	88	965	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	77.1989	92	965	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	77.181	74	965	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	76.9108	62	965	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:56:46,411] [INFO] DFAST Taxonomy check result was written to GCF_009695765.1_ASM969576v1_genomic.fna/tc_result.tsv
[2024-01-24 13:56:46,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:56:46,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:56:46,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/checkm_data
[2024-01-24 13:56:46,414] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:56:46,448] [INFO] Task started: CheckM
[2024-01-24 13:56:46,448] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009695765.1_ASM969576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009695765.1_ASM969576v1_genomic.fna/checkm_input GCF_009695765.1_ASM969576v1_genomic.fna/checkm_result
[2024-01-24 13:57:14,599] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:14,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:14,624] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:14,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:14,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009695765.1_ASM969576v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:14,626] [INFO] Task started: Blastn
[2024-01-24 13:57:14,626] [INFO] Running command: blastn -query GCF_009695765.1_ASM969576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7e1e530f-4cde-469a-bec4-f58e4ce23e57/dqc_reference/reference_markers_gtdb.fasta -out GCF_009695765.1_ASM969576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:15,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:15,828] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:15,828] [INFO] Target genome list was writen to GCF_009695765.1_ASM969576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:16,628] [INFO] Task started: fastANI
[2024-01-24 13:57:16,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgf925455f-3fd3-4f90-9d11-30de418afcbb/GCF_009695765.1_ASM969576v1_genomic.fna.gz --refList GCF_009695765.1_ASM969576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009695765.1_ASM969576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:27,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:27,880] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:27,881] [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_009695765.1	s__VUNI01 sp009695765	100.0	962	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__VUNI01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001940165.1	s__Roseburia sp001940165	80.0351	196	965	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_902363675.1	s__Agathobacter sp000434275	79.1173	244	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.18	99.14	0.93	0.89	5	-
GCF_001406815.1	s__Agathobacter faecis	78.8117	237	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.10	97.07	0.85	0.62	43	-
GCF_000174195.1	s__Roseburia inulinivorans	78.7898	217	965	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_900537995.1	s__Roseburia intestinalis	78.761	211	965	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_003470905.1	s__Roseburia sp003470905	78.5122	208	965	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_002474415.1	s__Agathobacter sp002474415	78.4005	147	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550545.1	s__Agathobacter sp900550545	78.3592	205	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552085.1	s__Agathobacter sp900552085	78.3548	185	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	97.03	95.54	0.78	0.69	7	-
GCA_905209075.1	s__Agathobacter sp905209075	78.3159	146	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	98.22	97.67	0.80	0.73	5	-
GCA_017623935.1	s__Agathobacter sp017623935	78.309	147	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.03	99.03	0.82	0.82	2	-
GCA_003483745.1	s__Roseburia sp003483745	78.2567	190	965	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_003122485.1	s__Eubacterium_I ramulus_A	78.0776	135	965	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_900550935.1	s__Roseburia sp900550935	77.9234	146	965	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_900543445.1	s__Agathobacter sp900543445	77.7165	177	965	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_003507655.1	s__UBA11774 sp003507655	77.7076	116	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA11774	95.0	98.49	98.09	0.91	0.83	6	-
GCA_900316805.1	s__Agathobacter sp900316805	76.9875	119	965	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Agathobacter	95.0	99.85	99.74	0.94	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:27,882] [INFO] GTDB search result was written to GCF_009695765.1_ASM969576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:27,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:27,887] [INFO] DFAST_QC result json was written to GCF_009695765.1_ASM969576v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:27,888] [INFO] DFAST_QC completed!
[2024-01-24 13:57:27,888] [INFO] Total running time: 0h1m0s