[2024-01-24 14:20:14,522] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:14,524] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:14,524] [INFO] DQC Reference Directory: /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference
[2024-01-24 14:20:15,885] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:15,886] [INFO] Task started: Prodigal
[2024-01-24 14:20:15,886] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc42bef5-6ccb-4b05-908b-f08fde297fd4/GCF_008691045.1_ASM869104v1_genomic.fna.gz | prodigal -d GCF_008691045.1_ASM869104v1_genomic.fna/cds.fna -a GCF_008691045.1_ASM869104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:24,029] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:24,030] [INFO] Task started: HMMsearch
[2024-01-24 14:20:24,030] [INFO] Running command: hmmsearch --tblout GCF_008691045.1_ASM869104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/reference_markers.hmm GCF_008691045.1_ASM869104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:24,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:24,303] [INFO] Found 6/6 markers.
[2024-01-24 14:20:24,335] [INFO] Query marker FASTA was written to GCF_008691045.1_ASM869104v1_genomic.fna/markers.fasta
[2024-01-24 14:20:24,335] [INFO] Task started: Blastn
[2024-01-24 14:20:24,336] [INFO] Running command: blastn -query GCF_008691045.1_ASM869104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/reference_markers.fasta -out GCF_008691045.1_ASM869104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:25,029] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:25,033] [INFO] Selected 21 target genomes.
[2024-01-24 14:20:25,034] [INFO] Target genome list was writen to GCF_008691045.1_ASM869104v1_genomic.fna/target_genomes.txt
[2024-01-24 14:20:25,076] [INFO] Task started: fastANI
[2024-01-24 14:20:25,076] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc42bef5-6ccb-4b05-908b-f08fde297fd4/GCF_008691045.1_ASM869104v1_genomic.fna.gz --refList GCF_008691045.1_ASM869104v1_genomic.fna/target_genomes.txt --output GCF_008691045.1_ASM869104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:36,088] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:36,088] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:36,089] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:36,102] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:20:36,103] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:20:36,103] [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
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	100.0	1032	1032	95	conclusive
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	79.5359	145	1032	95	below_threshold
[Ruminococcus] torques	strain=ATCC 27756	GCA_000153925.1	33039	33039	type	True	78.6985	201	1032	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_000155205.1	46228	46228	type	True	78.4125	181	1032	95	below_threshold
[Ruminococcus] lactaris	strain=ATCC 29176	GCA_025152405.1	46228	46228	type	True	78.3412	190	1032	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	78.2099	112	1032	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_025150245.1	39486	39486	suspected-type	True	77.9764	101	1032	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	77.9668	88	1032	95	below_threshold
Dorea formicigenerans	strain=ATCC 27755	GCA_000169235.1	39486	39486	suspected-type	True	77.9523	104	1032	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_000156535.1	166486	166486	type	True	77.8797	72	1032	95	below_threshold
Roseburia intestinalis	strain=L1 82	GCA_025151715.1	166486	166486	type	True	77.8316	78	1032	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.7778	135	1032	95	below_threshold
Roseburia intestinalis	strain=L1-82	GCA_900537995.1	166486	166486	type	True	77.6226	75	1032	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	77.5985	171	1032	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	77.5775	172	1032	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	77.5643	181	1032	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	77.5523	173	1032	95	below_threshold
Muricomes intestini	strain=DSM 29489	GCA_004346165.1	1796634	1796634	type	True	77.4595	97	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:36,104] [INFO] DFAST Taxonomy check result was written to GCF_008691045.1_ASM869104v1_genomic.fna/tc_result.tsv
[2024-01-24 14:20:36,105] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:36,105] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:36,105] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/checkm_data
[2024-01-24 14:20:36,106] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:36,141] [INFO] Task started: CheckM
[2024-01-24 14:20:36,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008691045.1_ASM869104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008691045.1_ASM869104v1_genomic.fna/checkm_input GCF_008691045.1_ASM869104v1_genomic.fna/checkm_result
[2024-01-24 14:21:04,829] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:04,830] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:04,851] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:04,851] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:04,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008691045.1_ASM869104v1_genomic.fna/markers.fasta)
[2024-01-24 14:21:04,852] [INFO] Task started: Blastn
[2024-01-24 14:21:04,853] [INFO] Running command: blastn -query GCF_008691045.1_ASM869104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc13fe388-5f38-48c2-b5ff-6e0405a0c771/dqc_reference/reference_markers_gtdb.fasta -out GCF_008691045.1_ASM869104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:05,994] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:05,998] [INFO] Selected 12 target genomes.
[2024-01-24 14:21:05,998] [INFO] Target genome list was writen to GCF_008691045.1_ASM869104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:06,033] [INFO] Task started: fastANI
[2024-01-24 14:21:06,033] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc42bef5-6ccb-4b05-908b-f08fde297fd4/GCF_008691045.1_ASM869104v1_genomic.fna.gz --refList GCF_008691045.1_ASM869104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008691045.1_ASM869104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:13,253] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:13,268] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:13,269] [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_002159505.1	s__Mediterraneibacter ornithocaccae	98.2875	863	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.93	97.52	0.83	0.82	3	conclusive
GCA_019119675.1	s__Mediterraneibacter faecipullorum	85.226	597	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119265.1	s__Mediterraneibacter intestinigallinarum	83.1577	504	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119995.1	s__Mediterraneibacter faecavium	82.9366	580	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.90	99.90	0.92	0.92	2	-
GCA_904377845.1	s__Mediterraneibacter sp904377845	82.6373	593	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119745.1	s__Mediterraneibacter gallistercoris	82.2802	470	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118885.1	s__Mediterraneibacter surreyensis	81.5407	504	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	98.86	98.12	0.80	0.76	3	-
GCA_019116885.1	s__Mediterraneibacter pullistercoris	80.8484	417	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	99.20	99.20	0.93	0.93	2	-
GCA_019120275.1	s__Mediterraneibacter excrementavium	79.8157	368	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904418845.1	s__Mediterraneibacter sp904418845	78.9975	274	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019120075.1	s__Mediterraneibacter excrementigallinarum_A	78.9513	343	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	97.40	96.45	0.78	0.77	3	-
GCA_019120595.1	s__Mediterraneibacter tabaqchaliae	78.8548	321	1032	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Mediterraneibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:13,271] [INFO] GTDB search result was written to GCF_008691045.1_ASM869104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:13,271] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:13,275] [INFO] DFAST_QC result json was written to GCF_008691045.1_ASM869104v1_genomic.fna/dqc_result.json
[2024-01-24 14:21:13,275] [INFO] DFAST_QC completed!
[2024-01-24 14:21:13,275] [INFO] Total running time: 0h0m59s