[2024-01-25 18:57:35,731] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:57:35,732] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:57:35,733] [INFO] DQC Reference Directory: /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference
[2024-01-25 18:57:36,851] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:57:36,851] [INFO] Task started: Prodigal
[2024-01-25 18:57:36,852] [INFO] Running command: gunzip -c /var/lib/cwl/stg1aa77fd6-60e2-4000-8a89-30ce0bf47104/GCF_900155735.1_ASM90015573v1_genomic.fna.gz | prodigal -d GCF_900155735.1_ASM90015573v1_genomic.fna/cds.fna -a GCF_900155735.1_ASM90015573v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:57:44,120] [INFO] Task succeeded: Prodigal
[2024-01-25 18:57:44,121] [INFO] Task started: HMMsearch
[2024-01-25 18:57:44,121] [INFO] Running command: hmmsearch --tblout GCF_900155735.1_ASM90015573v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/reference_markers.hmm GCF_900155735.1_ASM90015573v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:57:44,347] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:57:44,348] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1aa77fd6-60e2-4000-8a89-30ce0bf47104/GCF_900155735.1_ASM90015573v1_genomic.fna.gz]
[2024-01-25 18:57:44,375] [INFO] Query marker FASTA was written to GCF_900155735.1_ASM90015573v1_genomic.fna/markers.fasta
[2024-01-25 18:57:44,375] [INFO] Task started: Blastn
[2024-01-25 18:57:44,375] [INFO] Running command: blastn -query GCF_900155735.1_ASM90015573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/reference_markers.fasta -out GCF_900155735.1_ASM90015573v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:45,033] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:45,036] [INFO] Selected 15 target genomes.
[2024-01-25 18:57:45,036] [INFO] Target genome list was writen to GCF_900155735.1_ASM90015573v1_genomic.fna/target_genomes.txt
[2024-01-25 18:57:45,051] [INFO] Task started: fastANI
[2024-01-25 18:57:45,051] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aa77fd6-60e2-4000-8a89-30ce0bf47104/GCF_900155735.1_ASM90015573v1_genomic.fna.gz --refList GCF_900155735.1_ASM90015573v1_genomic.fna/target_genomes.txt --output GCF_900155735.1_ASM90015573v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:57:52,860] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:52,861] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:57:52,861] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:57:52,869] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:57:52,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:57:52,870] [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
Intestinibacillus massiliensis	strain=type strain: Marseille-P3216	GCA_900155735.1	1871029	1871029	type	True	99.9999	928	931	95	conclusive
Agathobaculum desmolans	strain=ATCC 43058	GCA_000701665.1	39484	39484	type	True	78.2551	186	931	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_014648015.1	1712515	1712515	type	True	78.2251	198	931	95	below_threshold
Ligaoa zhengdingensis	strain=NSJ-31	GCA_014384885.1	2763658	2763658	type	True	78.1624	65	931	95	below_threshold
Butyricicoccus faecihominis	strain=JCM 31056	GCA_016586375.1	1712515	1712515	type	True	78.155	202	931	95	below_threshold
Butyricicoccus pullicaecorum	strain=DSM 23266	GCA_900167005.1	501571	501571	type	True	77.9925	170	931	95	below_threshold
Butyricicoccus porcorum	strain=BB10	GCA_002157465.1	1945634	1945634	type	True	77.7693	117	931	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.8144	93	931	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.7756	68	931	95	below_threshold
Faecalibacterium hattorii	strain=APC922/41-1	GCA_003287455.1	2935520	2935520	type	True	76.2056	53	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:57:52,872] [INFO] DFAST Taxonomy check result was written to GCF_900155735.1_ASM90015573v1_genomic.fna/tc_result.tsv
[2024-01-25 18:57:52,872] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:57:52,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:57:52,872] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/checkm_data
[2024-01-25 18:57:52,873] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:57:52,901] [INFO] Task started: CheckM
[2024-01-25 18:57:52,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155735.1_ASM90015573v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155735.1_ASM90015573v1_genomic.fna/checkm_input GCF_900155735.1_ASM90015573v1_genomic.fna/checkm_result
[2024-01-25 18:58:18,202] [INFO] Task succeeded: CheckM
[2024-01-25 18:58:18,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:58:18,217] [INFO] ===== Completeness check finished =====
[2024-01-25 18:58:18,217] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:58:18,218] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155735.1_ASM90015573v1_genomic.fna/markers.fasta)
[2024-01-25 18:58:18,218] [INFO] Task started: Blastn
[2024-01-25 18:58:18,218] [INFO] Running command: blastn -query GCF_900155735.1_ASM90015573v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd69e1a59-dcb6-48a6-b316-23ef91d5c06e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155735.1_ASM90015573v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:58:19,449] [INFO] Task succeeded: Blastn
[2024-01-25 18:58:19,452] [INFO] Selected 16 target genomes.
[2024-01-25 18:58:19,452] [INFO] Target genome list was writen to GCF_900155735.1_ASM90015573v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:58:19,466] [INFO] Task started: fastANI
[2024-01-25 18:58:19,466] [INFO] Running command: fastANI --query /var/lib/cwl/stg1aa77fd6-60e2-4000-8a89-30ce0bf47104/GCF_900155735.1_ASM90015573v1_genomic.fna.gz --refList GCF_900155735.1_ASM90015573v1_genomic.fna/target_genomes_gtdb.txt --output GCF_900155735.1_ASM90015573v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:58:26,767] [INFO] Task succeeded: fastANI
[2024-01-25 18:58:26,777] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:58:26,777] [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_900155735.1	s__Intestinibacillus massiliensis	99.9999	928	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Intestinibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900555465.1	s__Agathobaculum intestinigallinarum	79.8806	184	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.06	97.06	0.83	0.83	2	-
GCA_004552245.1	s__Butyricicoccus sp004552245	79.3341	184	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900625105.1	s__Agathobaculum sp900625105	79.1858	273	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113065.1	s__Agathobaculum stercoravium	79.1723	241	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.25	98.25	0.89	0.89	2	-
GCA_900544475.1	s__Agathobaculum sp900544475	79.0613	187	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	97.90	97.82	0.89	0.86	3	-
GCF_900291975.1	s__Agathobaculum sp900291975	78.9596	242	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	99.23	99.13	0.90	0.87	7	-
GCA_019114345.1	s__Agathobaculum pullistercoris	78.9409	207	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.72	98.13	0.86	0.78	4	-
GCA_900557315.1	s__Agathobaculum sp900557315	78.8032	171	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	100.00	100.00	0.98	0.98	2	-
GCA_019119435.1	s__Butyricicoccus avicola	78.7951	157	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	98.92	98.91	0.91	0.91	3	-
GCA_019115185.1	s__Agathobaculum merdipullorum	78.6041	167	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019112985.1	s__Butyricicoccus_A stercorigallinarum	78.2676	190	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900604335.1	s__Butyricicoccus sp900604335	78.2657	176	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Butyricicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000701665.1	s__Agathobaculum desmolans	78.2551	186	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__Agathobaculum	95.0	98.85	98.85	0.90	0.90	2	-
GCA_910586105.1	s__QXXE01 sp910586105	78.1792	166	931	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Butyricicoccaceae;g__QXXE01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:58:26,779] [INFO] GTDB search result was written to GCF_900155735.1_ASM90015573v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:58:26,779] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:58:26,782] [INFO] DFAST_QC result json was written to GCF_900155735.1_ASM90015573v1_genomic.fna/dqc_result.json
[2024-01-25 18:58:26,782] [INFO] DFAST_QC completed!
[2024-01-25 18:58:26,782] [INFO] Total running time: 0h0m51s