[2024-01-24 13:55:14,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:55:14,225] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:55:14,226] [INFO] DQC Reference Directory: /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference
[2024-01-24 13:55:15,604] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:55:15,605] [INFO] Task started: Prodigal
[2024-01-24 13:55:15,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d611d47-7502-47fc-8aff-17afbe5a7a02/GCF_014287925.1_ASM1428792v1_genomic.fna.gz | prodigal -d GCF_014287925.1_ASM1428792v1_genomic.fna/cds.fna -a GCF_014287925.1_ASM1428792v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:55:23,830] [INFO] Task succeeded: Prodigal
[2024-01-24 13:55:23,831] [INFO] Task started: HMMsearch
[2024-01-24 13:55:23,831] [INFO] Running command: hmmsearch --tblout GCF_014287925.1_ASM1428792v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/reference_markers.hmm GCF_014287925.1_ASM1428792v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:55:24,088] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:55:24,089] [INFO] Found 6/6 markers.
[2024-01-24 13:55:24,125] [INFO] Query marker FASTA was written to GCF_014287925.1_ASM1428792v1_genomic.fna/markers.fasta
[2024-01-24 13:55:24,125] [INFO] Task started: Blastn
[2024-01-24 13:55:24,126] [INFO] Running command: blastn -query GCF_014287925.1_ASM1428792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/reference_markers.fasta -out GCF_014287925.1_ASM1428792v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:55:24,814] [INFO] Task succeeded: Blastn
[2024-01-24 13:55:24,818] [INFO] Selected 22 target genomes.
[2024-01-24 13:55:24,819] [INFO] Target genome list was writen to GCF_014287925.1_ASM1428792v1_genomic.fna/target_genomes.txt
[2024-01-24 13:55:24,856] [INFO] Task started: fastANI
[2024-01-24 13:55:24,856] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d611d47-7502-47fc-8aff-17afbe5a7a02/GCF_014287925.1_ASM1428792v1_genomic.fna.gz --refList GCF_014287925.1_ASM1428792v1_genomic.fna/target_genomes.txt --output GCF_014287925.1_ASM1428792v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:55:39,199] [INFO] Task succeeded: fastANI
[2024-01-24 13:55:39,200] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:55:39,200] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:55:39,218] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:55:39,218] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:55:39,219] [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
Clostridium fessum	strain=SNUG30386	GCA_003024715.1	2126740	2126740	type	True	98.0328	889	1024	95	conclusive
Roseburia hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	82.615	131	1024	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.8277	82	1024	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	79.9644	52	1024	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	79.8623	52	1024	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	79.8623	82	1024	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	79.7991	86	1024	95	below_threshold
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	79.7968	102	1024	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	79.6823	107	1024	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	79.6817	86	1024	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.66	83	1024	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	79.3785	102	1024	95	below_threshold
[Clostridium] aminophilum	strain=F	GCA_900112885.1	1526	1526	type	True	78.0879	107	1024	95	below_threshold
[Clostridium] aminophilum	strain=DSM 10710	GCA_000711825.1	1526	1526	type	True	78.0375	107	1024	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	77.1867	121	1024	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.8811	96	1024	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.7316	98	1024	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:55:39,220] [INFO] DFAST Taxonomy check result was written to GCF_014287925.1_ASM1428792v1_genomic.fna/tc_result.tsv
[2024-01-24 13:55:39,221] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:55:39,221] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:55:39,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/checkm_data
[2024-01-24 13:55:39,223] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:55:39,259] [INFO] Task started: CheckM
[2024-01-24 13:55:39,259] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014287925.1_ASM1428792v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014287925.1_ASM1428792v1_genomic.fna/checkm_input GCF_014287925.1_ASM1428792v1_genomic.fna/checkm_result
[2024-01-24 13:56:10,002] [INFO] Task succeeded: CheckM
[2024-01-24 13:56:10,003] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:56:10,024] [INFO] ===== Completeness check finished =====
[2024-01-24 13:56:10,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:56:10,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014287925.1_ASM1428792v1_genomic.fna/markers.fasta)
[2024-01-24 13:56:10,025] [INFO] Task started: Blastn
[2024-01-24 13:56:10,025] [INFO] Running command: blastn -query GCF_014287925.1_ASM1428792v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb0b02272-de50-4a2a-a5fa-d10d61693ae3/dqc_reference/reference_markers_gtdb.fasta -out GCF_014287925.1_ASM1428792v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:56:11,221] [INFO] Task succeeded: Blastn
[2024-01-24 13:56:11,230] [INFO] Selected 22 target genomes.
[2024-01-24 13:56:11,231] [INFO] Target genome list was writen to GCF_014287925.1_ASM1428792v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:56:11,264] [INFO] Task started: fastANI
[2024-01-24 13:56:11,264] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d611d47-7502-47fc-8aff-17afbe5a7a02/GCF_014287925.1_ASM1428792v1_genomic.fna.gz --refList GCF_014287925.1_ASM1428792v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014287925.1_ASM1428792v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:56:25,811] [INFO] Task succeeded: fastANI
[2024-01-24 13:56:25,833] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:56:25,833] [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_003024715.1	s__Clostridium_Q fessum	98.0328	889	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.33	97.70	0.88	0.81	31	conclusive
GCA_003478355.1	s__UBA3402 sp003478355	83.0541	228	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	97.92	96.21	0.85	0.69	6	-
GCF_003478505.1	s__Ventrimonas sp003478505	82.8243	217	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.07	97.61	0.91	0.78	6	-
GCF_003435375.1	s__Copromonas sp900066535	81.8128	239	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Copromonas	95.0	97.23	95.52	0.82	0.74	22	-
GCF_003481825.1	s__Ventrimonas sp003481825	81.3174	185	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.33	98.65	0.93	0.87	3	-
GCF_003480315.1	s__Ventrimonas sp003480315	79.9884	192	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.62	98.00	0.91	0.88	5	-
GCA_016302185.1	s__Clostridium_Q sp016302185	78.3779	186	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555625.1	s__Ventrimonas sp900555625	78.2727	93	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.73	98.70	0.86	0.85	3	-
GCA_900547735.1	s__Clostridium_Q sp900547735	78.2069	182	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018377235.1	s__Clostridium_Q sp018377235	78.1174	131	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626075.1	s__Clostridium_Q transplantifaecale	78.0883	180	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000466485.1	s__Clostridium_Q symbiosum	77.9717	182	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.86	98.57	0.86	0.81	32	-
GCA_900538475.1	s__Ventrimonas sp900538475	77.7954	98	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.39	99.20	0.94	0.93	3	-
GCA_900770345.1	s__Enterocloster sp900770345	77.6512	95	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770535.1	s__Ventrimonas sp900770535	77.5198	96	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	98.72	98.72	0.86	0.86	2	-
GCA_009911305.1	s__Clostridium_Q sp009911305	77.4189	184	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Clostridium_Q	95.0	98.99	98.99	0.91	0.91	2	-
GCA_900540335.1	s__Ventrimonas sp900540335	77.3382	90	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.37	99.36	0.86	0.81	3	-
GCA_001304875.1	s__Ventrisoma faecale	77.2753	147	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrisoma	95.0	98.23	97.74	0.91	0.86	4	-
GCF_000235505.1	s__Hungatella_A hathewayi_A	77.2422	103	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Hungatella_A	95.0	99.27	96.59	0.97	0.86	6	-
GCA_004554205.1	s__Ventrimonas sp004554205	76.6319	81	1024	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:56:25,835] [INFO] GTDB search result was written to GCF_014287925.1_ASM1428792v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:56:25,835] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:56:25,840] [INFO] DFAST_QC result json was written to GCF_014287925.1_ASM1428792v1_genomic.fna/dqc_result.json
[2024-01-24 13:56:25,840] [INFO] DFAST_QC completed!
[2024-01-24 13:56:25,840] [INFO] Total running time: 0h1m12s