[2024-01-24 11:35:23,593] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:23,597] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:23,598] [INFO] DQC Reference Directory: /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference
[2024-01-24 11:35:26,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:26,250] [INFO] Task started: Prodigal
[2024-01-24 11:35:26,251] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d34611c-20f9-4986-a1e8-674378fc5226/GCF_025567365.1_ASM2556736v1_genomic.fna.gz | prodigal -d GCF_025567365.1_ASM2556736v1_genomic.fna/cds.fna -a GCF_025567365.1_ASM2556736v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:31,794] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:31,794] [INFO] Task started: HMMsearch
[2024-01-24 11:35:31,794] [INFO] Running command: hmmsearch --tblout GCF_025567365.1_ASM2556736v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/reference_markers.hmm GCF_025567365.1_ASM2556736v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:32,079] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:32,080] [INFO] Found 6/6 markers.
[2024-01-24 11:35:32,110] [INFO] Query marker FASTA was written to GCF_025567365.1_ASM2556736v1_genomic.fna/markers.fasta
[2024-01-24 11:35:32,110] [INFO] Task started: Blastn
[2024-01-24 11:35:32,111] [INFO] Running command: blastn -query GCF_025567365.1_ASM2556736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/reference_markers.fasta -out GCF_025567365.1_ASM2556736v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:33,011] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:33,015] [INFO] Selected 24 target genomes.
[2024-01-24 11:35:33,016] [INFO] Target genome list was writen to GCF_025567365.1_ASM2556736v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:33,045] [INFO] Task started: fastANI
[2024-01-24 11:35:33,045] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d34611c-20f9-4986-a1e8-674378fc5226/GCF_025567365.1_ASM2556736v1_genomic.fna.gz --refList GCF_025567365.1_ASM2556736v1_genomic.fna/target_genomes.txt --output GCF_025567365.1_ASM2556736v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:46,600] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:46,600] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:46,601] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:46,618] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:46,618] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:46,618] [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
Anaerostipes hadrus	strain=DSM 3319	GCA_000332875.2	649756	649756	type	True	88.8419	614	810	95	below_threshold
Coprococcus comes	strain=ATCC 27758	GCA_025149785.1	410072	410072	type	True	79.4501	95	810	95	below_threshold
Anaerostipes faecalis	strain=AGMB03513	GCA_018982945.1	2738446	2738446	type	True	79.3802	280	810	95	below_threshold
Eubacterium ramulus	strain=ATCC 29099	GCA_000469345.1	39490	39490	type	True	78.6777	67	810	95	below_threshold
Anaerostipes butyraticus	strain=JCM 17466	GCA_016586355.1	645466	645466	type	True	78.4961	211	810	95	below_threshold
Anaerostipes caccae	strain=JCM 13470	GCA_014467075.1	105841	105841	type	True	78.1809	92	810	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_000154305.1	105841	105841	type	True	78.0981	95	810	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	78.0891	91	810	95	below_threshold
Anaerostipes caccae	strain=DSM 14662	GCA_025146005.1	105841	105841	type	True	78.0742	92	810	95	below_threshold
Anaerostipes rhamnosivorans	strain=1y2	GCA_005280655.1	1229621	1229621	type	True	78.0234	92	810	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	77.8249	84	810	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	77.8042	57	810	95	below_threshold
Anaerobutyricum hallii	strain=DSM 3353	GCA_000173975.1	39488	39488	type	True	77.7288	88	810	95	below_threshold
Coprococcus phoceensis	strain=Marseille-P3062	GCA_900104635.1	1870993	1870993	type	True	77.5577	61	810	95	below_threshold
[Clostridium] polysaccharolyticum	strain=DSM 1801	GCA_900111595.1	29364	29364	type	True	76.9374	50	810	95	below_threshold
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	76.6626	56	810	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:46,620] [INFO] DFAST Taxonomy check result was written to GCF_025567365.1_ASM2556736v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:46,621] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:46,621] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:46,621] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/checkm_data
[2024-01-24 11:35:46,622] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:46,648] [INFO] Task started: CheckM
[2024-01-24 11:35:46,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025567365.1_ASM2556736v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025567365.1_ASM2556736v1_genomic.fna/checkm_input GCF_025567365.1_ASM2556736v1_genomic.fna/checkm_result
[2024-01-24 11:36:10,674] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:10,676] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:10,698] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:10,698] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:10,699] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025567365.1_ASM2556736v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:10,699] [INFO] Task started: Blastn
[2024-01-24 11:36:10,700] [INFO] Running command: blastn -query GCF_025567365.1_ASM2556736v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8289a8d7-64cb-422a-bc6b-d76ed26029e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_025567365.1_ASM2556736v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:11,746] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:11,750] [INFO] Selected 8 target genomes.
[2024-01-24 11:36:11,750] [INFO] Target genome list was writen to GCF_025567365.1_ASM2556736v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:11,757] [INFO] Task started: fastANI
[2024-01-24 11:36:11,758] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d34611c-20f9-4986-a1e8-674378fc5226/GCF_025567365.1_ASM2556736v1_genomic.fna.gz --refList GCF_025567365.1_ASM2556736v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025567365.1_ASM2556736v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:16,431] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:16,444] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:16,444] [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_001404655.1	s__Anaerostipes hadrus_A	100.0	808	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.11	98.66	0.92	0.88	9	conclusive
GCA_902362875.1	s__Anaerostipes sp900066705	91.3632	674	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.16	98.31	0.96	0.92	3	-
GCF_000332875.2	s__Anaerostipes hadrus	88.8419	614	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	98.35	97.09	0.85	0.65	78	-
GCA_905215045.1	s__Anaerostipes sp905215045	88.6663	422	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918155.1	s__Anaerostipes sp018918155	80.9579	363	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001940315.1	s__Anaerostipes sp001940315	79.3186	286	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	99.20	99.20	0.89	0.89	2	-
GCA_900756035.1	s__Anaerostipes sp900756035	78.9044	247	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019119895.1	s__Anaerostipes avistercoris	78.6334	202	810	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Anaerostipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:16,446] [INFO] GTDB search result was written to GCF_025567365.1_ASM2556736v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:16,446] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:16,449] [INFO] DFAST_QC result json was written to GCF_025567365.1_ASM2556736v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:16,449] [INFO] DFAST_QC completed!
[2024-01-24 11:36:16,450] [INFO] Total running time: 0h0m53s