[2024-01-24 13:28:25,940] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:28:25,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:28:25,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference
[2024-01-24 13:28:27,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:28:27,427] [INFO] Task started: Prodigal
[2024-01-24 13:28:27,428] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0a42094-92f3-4feb-a4ea-a393d52191a1/GCF_013201155.1_ASM1320115v1_genomic.fna.gz | prodigal -d GCF_013201155.1_ASM1320115v1_genomic.fna/cds.fna -a GCF_013201155.1_ASM1320115v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:33,612] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:33,612] [INFO] Task started: HMMsearch
[2024-01-24 13:28:33,613] [INFO] Running command: hmmsearch --tblout GCF_013201155.1_ASM1320115v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/reference_markers.hmm GCF_013201155.1_ASM1320115v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:33,857] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:33,859] [INFO] Found 6/6 markers.
[2024-01-24 13:28:33,878] [INFO] Query marker FASTA was written to GCF_013201155.1_ASM1320115v1_genomic.fna/markers.fasta
[2024-01-24 13:28:33,878] [INFO] Task started: Blastn
[2024-01-24 13:28:33,878] [INFO] Running command: blastn -query GCF_013201155.1_ASM1320115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/reference_markers.fasta -out GCF_013201155.1_ASM1320115v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:34,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:34,584] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:34,585] [INFO] Target genome list was writen to GCF_013201155.1_ASM1320115v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:34,601] [INFO] Task started: fastANI
[2024-01-24 13:28:34,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a42094-92f3-4feb-a4ea-a393d52191a1/GCF_013201155.1_ASM1320115v1_genomic.fna.gz --refList GCF_013201155.1_ASM1320115v1_genomic.fna/target_genomes.txt --output GCF_013201155.1_ASM1320115v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:41,817] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:41,817] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:41,817] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:41,831] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:41,831] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:41,831] [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
Berryella wangjianweii	strain=zg-1050	GCA_013201155.1	2734634	2734634	type	True	100.0	601	601	95	conclusive
Berryella intestinalis	strain=68-1-3	GCA_000814825.1	1531429	1531429	type	True	80.0416	305	601	95	below_threshold
Gordonibacter pamelaeae	strain=7-10-1-bT	GCA_000210055.1	471189	471189	type	True	79.0009	227	601	95	below_threshold
Eggerthella guodeyinii	strain=HF-1101	GCA_009834925.2	2690837	2690837	type	True	78.9146	274	601	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213T	GCA_900199375.1	1335613	1335613	type	True	78.8801	236	601	95	below_threshold
Gordonibacter urolithinfaciens	strain=DSM 27213	GCA_003788975.1	1335613	1335613	type	True	78.8233	238	601	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_000024265.1	84112	84112	type	True	78.6968	244	601	95	below_threshold
Eggerthella lenta	strain=ATCC 25559	GCA_003340105.1	84112	84112	type	True	78.6722	246	601	95	below_threshold
Eggerthella lenta	strain=DSM 2243	GCA_003339975.1	84112	84112	type	True	78.6301	248	601	95	below_threshold
Eggerthella lenta	strain=UCSF2243	GCA_003339945.1	84112	84112	type	True	78.6168	249	601	95	below_threshold
Eggerthella timonensis	strain=Marseille-P3135	GCA_900184265.1	1871008	1871008	type	True	78.6054	267	601	95	below_threshold
Eggerthella sinensis	strain=DSM 16107	GCA_003725965.1	242230	242230	type	True	78.4542	243	601	95	below_threshold
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	78.4375	182	601	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	78.3599	185	601	95	below_threshold
Xiamenia xianingshaonis	strain=zg-886	GCA_017945865.1	2682776	2682776	type	True	78.1749	149	601	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,833] [INFO] DFAST Taxonomy check result was written to GCF_013201155.1_ASM1320115v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:41,833] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:41,833] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:41,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/checkm_data
[2024-01-24 13:28:41,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:41,857] [INFO] Task started: CheckM
[2024-01-24 13:28:41,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013201155.1_ASM1320115v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013201155.1_ASM1320115v1_genomic.fna/checkm_input GCF_013201155.1_ASM1320115v1_genomic.fna/checkm_result
[2024-01-24 13:29:05,437] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:05,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:05,458] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:05,458] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:05,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013201155.1_ASM1320115v1_genomic.fna/markers.fasta)
[2024-01-24 13:29:05,460] [INFO] Task started: Blastn
[2024-01-24 13:29:05,460] [INFO] Running command: blastn -query GCF_013201155.1_ASM1320115v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97984534-9dc5-48dd-aacf-2c6ea9a0b565/dqc_reference/reference_markers_gtdb.fasta -out GCF_013201155.1_ASM1320115v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:06,518] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:06,521] [INFO] Selected 16 target genomes.
[2024-01-24 13:29:06,521] [INFO] Target genome list was writen to GCF_013201155.1_ASM1320115v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:06,538] [INFO] Task started: fastANI
[2024-01-24 13:29:06,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0a42094-92f3-4feb-a4ea-a393d52191a1/GCF_013201155.1_ASM1320115v1_genomic.fna.gz --refList GCF_013201155.1_ASM1320115v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013201155.1_ASM1320115v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:13,628] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:13,642] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:13,642] [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
GCA_013201155.1	s__Berryella sp013201155	100.0	601	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Berryella	95.0	98.94	98.86	0.97	0.97	3	conclusive
GCF_000814825.1	s__Berryella intestinalis	79.9571	306	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Berryella	95.0	96.96	96.96	0.86	0.86	2	-
GCF_900604965.1	s__Berryella sp900604965	79.1719	241	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Berryella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185065.1	s__CAAEEV01 sp013185065	79.1248	205	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
GCA_018710945.1	s__Aphodovivens avistercoris	79.0615	221	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210055.1	s__Gordonibacter pamelaeae	78.9618	229	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.65	97.59	0.89	0.82	6	-
GCF_009834925.2	s__Eggerthella sp014287365	78.9459	272	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Eggerthella	95.0	97.74	96.91	0.89	0.85	3	-
GCF_902386925.1	s__Arabia massiliensis	78.9159	257	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900199375.1	s__Gordonibacter urolithinfaciens	78.8537	238	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Gordonibacter	95.0	98.27	97.45	0.89	0.82	14	-
GCA_900550385.1	s__Aphodovivens sp900550385	78.517	162	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Aphodovivens	95.0	99.66	99.66	0.86	0.86	2	-
GCA_910585575.1	s__Adlercreutzia sp910585575	78.4059	157	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903789375.1	s__CAIFEB01 sp903789375	78.2466	207	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAIFEB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904420215.1	s__CAJFUR01 sp904420215	77.9351	169	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAJFUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015062685.1	s__UBA9715 sp015062685	77.8867	139	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__UBA9715	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900554945.1	s__Ellagibacter sp900554945	76.8213	87	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Ellagibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314665.1	s__RUG033 sp900314665	76.7432	63	601	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__RUG033;g__RUG033	95.0	99.47	99.47	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:13,644] [INFO] GTDB search result was written to GCF_013201155.1_ASM1320115v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:13,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:13,649] [INFO] DFAST_QC result json was written to GCF_013201155.1_ASM1320115v1_genomic.fna/dqc_result.json
[2024-01-24 13:29:13,649] [INFO] DFAST_QC completed!
[2024-01-24 13:29:13,649] [INFO] Total running time: 0h0m48s