[2024-01-24 11:59:05,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:05,211] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:05,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference
[2024-01-24 11:59:06,397] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:06,398] [INFO] Task started: Prodigal
[2024-01-24 11:59:06,398] [INFO] Running command: gunzip -c /var/lib/cwl/stg94a8c773-f6dd-48da-87ce-3bc4df36ce37/GCF_900243045.1_PRJEB14662_genomic.fna.gz | prodigal -d GCF_900243045.1_PRJEB14662_genomic.fna/cds.fna -a GCF_900243045.1_PRJEB14662_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:24,302] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:24,302] [INFO] Task started: HMMsearch
[2024-01-24 11:59:24,303] [INFO] Running command: hmmsearch --tblout GCF_900243045.1_PRJEB14662_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/reference_markers.hmm GCF_900243045.1_PRJEB14662_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:24,652] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:24,654] [INFO] Found 6/6 markers.
[2024-01-24 11:59:24,717] [INFO] Query marker FASTA was written to GCF_900243045.1_PRJEB14662_genomic.fna/markers.fasta
[2024-01-24 11:59:24,717] [INFO] Task started: Blastn
[2024-01-24 11:59:24,717] [INFO] Running command: blastn -query GCF_900243045.1_PRJEB14662_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/reference_markers.fasta -out GCF_900243045.1_PRJEB14662_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:25,357] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:25,362] [INFO] Selected 18 target genomes.
[2024-01-24 11:59:25,363] [INFO] Target genome list was writen to GCF_900243045.1_PRJEB14662_genomic.fna/target_genomes.txt
[2024-01-24 11:59:25,383] [INFO] Task started: fastANI
[2024-01-24 11:59:25,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg94a8c773-f6dd-48da-87ce-3bc4df36ce37/GCF_900243045.1_PRJEB14662_genomic.fna.gz --refList GCF_900243045.1_PRJEB14662_genomic.fna/target_genomes.txt --output GCF_900243045.1_PRJEB14662_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:41,537] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:41,538] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:41,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:41,556] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:59:41,556] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:59:41,556] [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
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	100.0	2356	2362	95	inconclusive
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	96.5691	1497	2362	95	inconclusive
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.3063	85	2362	95	below_threshold
Eisenbergiella tayi	strain=DSM 26961	GCA_001881565.1	1432052	1432052	type	True	80.4855	1004	2362	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	80.1212	91	2362	95	below_threshold
Hungatella hathewayi	strain=DSM 13479	GCA_025149285.1	154046	154046	suspected-type	True	80.1098	156	2362	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	79.2724	151	2362	95	below_threshold
Diplocloster modestus	strain=ASD4241	GCA_019042245.1	2850322	2850322	type	True	78.4762	93	2362	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	78.3564	98	2362	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	78.3349	98	2362	95	below_threshold
Kineothrix alysoides	strain=KNHs209	GCA_000732725.1	1469948	1469948	type	True	77.396	93	2362	95	below_threshold
Blautia coccoides	strain=DSM 935	GCA_004340925.1	1532	1532	type	True	77.0807	104	2362	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	77.0089	65	2362	95	below_threshold
Hespellia stercorisuis	strain=DSM 15480	GCA_900142165.1	180311	180311	type	True	76.6954	61	2362	95	below_threshold
Kineothrix alysoides	strain=DSM 100556	GCA_004345255.1	1469948	1469948	type	True	76.6863	91	2362	95	below_threshold
Anaerocolumna xylanovorans	strain=DSM 12503	GCA_900143645.1	100134	100134	type	True	76.5096	50	2362	95	below_threshold
Cuneatibacter caecimuris	strain=DSM 29486	GCA_004216775.1	1796618	1796618	type	True	76.3869	79	2362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:41,558] [INFO] DFAST Taxonomy check result was written to GCF_900243045.1_PRJEB14662_genomic.fna/tc_result.tsv
[2024-01-24 11:59:41,559] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:41,559] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:41,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/checkm_data
[2024-01-24 11:59:41,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:41,628] [INFO] Task started: CheckM
[2024-01-24 11:59:41,628] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900243045.1_PRJEB14662_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900243045.1_PRJEB14662_genomic.fna/checkm_input GCF_900243045.1_PRJEB14662_genomic.fna/checkm_result
[2024-01-24 12:00:34,262] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:34,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:34,287] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:34,287] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:34,288] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900243045.1_PRJEB14662_genomic.fna/markers.fasta)
[2024-01-24 12:00:34,288] [INFO] Task started: Blastn
[2024-01-24 12:00:34,288] [INFO] Running command: blastn -query GCF_900243045.1_PRJEB14662_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbe485b9-0683-4061-94ae-7b0046efc20a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900243045.1_PRJEB14662_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:35,415] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:35,420] [INFO] Selected 13 target genomes.
[2024-01-24 12:00:35,420] [INFO] Target genome list was writen to GCF_900243045.1_PRJEB14662_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:35,449] [INFO] Task started: fastANI
[2024-01-24 12:00:35,449] [INFO] Running command: fastANI --query /var/lib/cwl/stg94a8c773-f6dd-48da-87ce-3bc4df36ce37/GCF_900243045.1_PRJEB14662_genomic.fna.gz --refList GCF_900243045.1_PRJEB14662_genomic.fna/target_genomes_gtdb.txt --output GCF_900243045.1_PRJEB14662_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:46,440] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:46,455] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:00:46,455] [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_009696275.1	s__Eisenbergiella porci	96.5691	1497	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.00	96.55	0.75	0.70	10	conclusive
GCF_003478085.1	s__Eisenbergiella sp003478085	80.9404	1021	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	99.95	99.91	0.98	0.96	6	-
GCF_001881565.1	s__Eisenbergiella tayi	80.5032	997	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.85	97.22	0.85	0.80	21	-
GCA_900548905.1	s__Eisenbergiella sp900548905	80.2574	916	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119595.1	s__Eisenbergiella merdavium	78.2474	387	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	98.10	98.10	0.87	0.87	2	-
GCA_019113175.1	s__Eisenbergiella stercoravium	77.9701	371	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	97.74	96.88	0.81	0.75	3	-
GCA_019120525.1	s__Eisenbergiella stercorigallinarum	77.3815	221	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904392525.1	s__Eisenbergiella sp904392525	77.2391	286	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Eisenbergiella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441865.1	s__CAG-194 sp002441865	77.0137	53	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-194	95.0	99.31	99.31	0.87	0.87	2	-
GCA_018385425.1	s__Acetatifactor sp018385425	76.7934	77	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	99.11	99.11	0.86	0.86	2	-
GCA_900755865.1	s__Acetatifactor sp900755865	76.6828	71	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.03	98.03	0.82	0.82	2	-
GCA_002490705.1	s__UBA3282 sp002490705	76.2167	97	2362	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3282	95.0	99.98	99.98	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:00:46,457] [INFO] GTDB search result was written to GCF_900243045.1_PRJEB14662_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:46,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:46,464] [INFO] DFAST_QC result json was written to GCF_900243045.1_PRJEB14662_genomic.fna/dqc_result.json
[2024-01-24 12:00:46,464] [INFO] DFAST_QC completed!
[2024-01-24 12:00:46,464] [INFO] Total running time: 0h1m41s