[2024-01-25 18:50:05,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:50:05,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:50:05,596] [INFO] DQC Reference Directory: /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference
[2024-01-25 18:50:06,718] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:50:06,718] [INFO] Task started: Prodigal
[2024-01-25 18:50:06,719] [INFO] Running command: gunzip -c /var/lib/cwl/stg096ab318-8289-458c-9e06-f956602b2968/GCF_025567015.1_ASM2556701v1_genomic.fna.gz | prodigal -d GCF_025567015.1_ASM2556701v1_genomic.fna/cds.fna -a GCF_025567015.1_ASM2556701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:50:15,972] [INFO] Task succeeded: Prodigal
[2024-01-25 18:50:15,973] [INFO] Task started: HMMsearch
[2024-01-25 18:50:15,973] [INFO] Running command: hmmsearch --tblout GCF_025567015.1_ASM2556701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/reference_markers.hmm GCF_025567015.1_ASM2556701v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:50:16,194] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:50:16,195] [INFO] Found 6/6 markers.
[2024-01-25 18:50:16,228] [INFO] Query marker FASTA was written to GCF_025567015.1_ASM2556701v1_genomic.fna/markers.fasta
[2024-01-25 18:50:16,228] [INFO] Task started: Blastn
[2024-01-25 18:50:16,228] [INFO] Running command: blastn -query GCF_025567015.1_ASM2556701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/reference_markers.fasta -out GCF_025567015.1_ASM2556701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:16,829] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:16,833] [INFO] Selected 27 target genomes.
[2024-01-25 18:50:16,833] [INFO] Target genome list was writen to GCF_025567015.1_ASM2556701v1_genomic.fna/target_genomes.txt
[2024-01-25 18:50:16,851] [INFO] Task started: fastANI
[2024-01-25 18:50:16,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg096ab318-8289-458c-9e06-f956602b2968/GCF_025567015.1_ASM2556701v1_genomic.fna.gz --refList GCF_025567015.1_ASM2556701v1_genomic.fna/target_genomes.txt --output GCF_025567015.1_ASM2556701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:50:36,010] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:36,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:50:36,011] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:50:36,021] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:50:36,021] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:50:36,021] [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 hominis	strain=A2-183	GCA_000225345.1	301301	301301	type	True	82.521	183	1339	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	80.7209	86	1339	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	80.534	110	1339	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	80.5058	88	1339	95	below_threshold
Eisenbergiella massiliensis	strain=AT11	GCA_900243045.1	1720294	1720294	type	True	80.0507	150	1339	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	79.8454	102	1339	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	78.9964	94	1339	95	below_threshold
Eisenbergiella porci	strain=WCA-389-WT-23B	GCA_009696275.1	2652274	2652274	type	True	78.619	145	1339	95	below_threshold
Hominisplanchenecus faecis	strain=CLA-AA-H246	GCA_020687205.1	2885351	2885351	type	True	78.085	87	1339	95	below_threshold
Enterocloster clostridioformis	strain=ATCC 25537	GCA_900113155.1	1531	1531	type	True	77.8709	65	1339	95	below_threshold
Schaedlerella arabinosiphila	strain=DSM 106076	GCA_003885045.1	2044587	2044587	type	True	77.5113	62	1339	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.3894	161	1339	95	below_threshold
Enterocloster clostridioformis	strain=NCTC11224	GCA_900447015.1	1531	1531	suspected-type	True	77.1725	70	1339	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_014131715.1	33035	33035	suspected-type	True	76.852	54	1339	95	below_threshold
Blautia producta	strain=JCM 1471	GCA_010669205.1	33035	33035	suspected-type	True	76.8377	52	1339	95	below_threshold
Blautia producta	strain=DSM 2950	GCA_000439125.1	33035	33035	suspected-type	True	76.1859	52	1339	95	below_threshold
Blautia producta	strain=ATCC 27340	GCA_000373885.1	33035	33035	suspected-type	True	76.1086	51	1339	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:50:36,023] [INFO] DFAST Taxonomy check result was written to GCF_025567015.1_ASM2556701v1_genomic.fna/tc_result.tsv
[2024-01-25 18:50:36,023] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:50:36,023] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:50:36,024] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/checkm_data
[2024-01-25 18:50:36,024] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:50:36,074] [INFO] Task started: CheckM
[2024-01-25 18:50:36,074] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567015.1_ASM2556701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567015.1_ASM2556701v1_genomic.fna/checkm_input GCF_025567015.1_ASM2556701v1_genomic.fna/checkm_result
[2024-01-25 18:51:07,092] [INFO] Task succeeded: CheckM
[2024-01-25 18:51:07,093] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:51:07,136] [INFO] ===== Completeness check finished =====
[2024-01-25 18:51:07,136] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:51:07,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567015.1_ASM2556701v1_genomic.fna/markers.fasta)
[2024-01-25 18:51:07,137] [INFO] Task started: Blastn
[2024-01-25 18:51:07,137] [INFO] Running command: blastn -query GCF_025567015.1_ASM2556701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfb8cc45f-addb-49dc-ba40-55cb84a1078d/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567015.1_ASM2556701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:51:09,041] [INFO] Task succeeded: Blastn
[2024-01-25 18:51:09,044] [INFO] Selected 11 target genomes.
[2024-01-25 18:51:09,044] [INFO] Target genome list was writen to GCF_025567015.1_ASM2556701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:51:09,055] [INFO] Task started: fastANI
[2024-01-25 18:51:09,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg096ab318-8289-458c-9e06-f956602b2968/GCF_025567015.1_ASM2556701v1_genomic.fna.gz --refList GCF_025567015.1_ASM2556701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567015.1_ASM2556701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:51:16,669] [INFO] Task succeeded: fastANI
[2024-01-25 18:51:16,676] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:51:16,676] [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_003584705.1	s__Acetatifactor sp900066565	97.4048	1087	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	98.01	97.56	0.88	0.80	26	conclusive
GCA_900772845.1	s__Acetatifactor sp900772845	89.5302	775	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	95.92	95.92	0.80	0.80	2	-
GCA_003447295.1	s__Acetatifactor sp003447295	88.5827	574	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	97.04	96.84	0.74	0.71	4	-
GCA_900771995.1	s__Acetatifactor sp900771995	88.5282	714	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009695995.1	s__Acetatifactor intestinalis	88.3852	761	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	96.98	96.46	0.81	0.76	18	-
GCA_002431915.1	s__Acetatifactor sp002431915	86.4516	672	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766575.1	s__Acetatifactor sp900766575	85.8955	467	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293615.1	s__Acetatifactor sp016293615	77.8766	140	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015056975.1	s__Acetatifactor sp015056975	77.799	146	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016303085.1	s__Acetatifactor sp016303085	77.3923	135	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002368865.1	s__Acetatifactor sp002368865	76.6567	132	1339	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Acetatifactor	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:51:16,686] [INFO] GTDB search result was written to GCF_025567015.1_ASM2556701v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:51:16,687] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:51:16,691] [INFO] DFAST_QC result json was written to GCF_025567015.1_ASM2556701v1_genomic.fna/dqc_result.json
[2024-01-25 18:51:16,691] [INFO] DFAST_QC completed!
[2024-01-25 18:51:16,691] [INFO] Total running time: 0h1m11s