[2024-01-24 12:44:10,887] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:10,891] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:10,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference
[2024-01-24 12:44:12,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:12,293] [INFO] Task started: Prodigal
[2024-01-24 12:44:12,293] [INFO] Running command: gunzip -c /var/lib/cwl/stga1e16101-e05b-4322-b5e2-30b1e44c5a63/GCF_020686995.1_ASM2068699v1_genomic.fna.gz | prodigal -d GCF_020686995.1_ASM2068699v1_genomic.fna/cds.fna -a GCF_020686995.1_ASM2068699v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:44:21,058] [INFO] Task succeeded: Prodigal
[2024-01-24 12:44:21,058] [INFO] Task started: HMMsearch
[2024-01-24 12:44:21,059] [INFO] Running command: hmmsearch --tblout GCF_020686995.1_ASM2068699v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/reference_markers.hmm GCF_020686995.1_ASM2068699v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:44:21,434] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:44:21,435] [INFO] Found 6/6 markers.
[2024-01-24 12:44:21,469] [INFO] Query marker FASTA was written to GCF_020686995.1_ASM2068699v1_genomic.fna/markers.fasta
[2024-01-24 12:44:21,469] [INFO] Task started: Blastn
[2024-01-24 12:44:21,469] [INFO] Running command: blastn -query GCF_020686995.1_ASM2068699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/reference_markers.fasta -out GCF_020686995.1_ASM2068699v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:44:22,164] [INFO] Task succeeded: Blastn
[2024-01-24 12:44:22,167] [INFO] Selected 17 target genomes.
[2024-01-24 12:44:22,168] [INFO] Target genome list was writen to GCF_020686995.1_ASM2068699v1_genomic.fna/target_genomes.txt
[2024-01-24 12:44:22,172] [INFO] Task started: fastANI
[2024-01-24 12:44:22,173] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e16101-e05b-4322-b5e2-30b1e44c5a63/GCF_020686995.1_ASM2068699v1_genomic.fna.gz --refList GCF_020686995.1_ASM2068699v1_genomic.fna/target_genomes.txt --output GCF_020686995.1_ASM2068699v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:44:32,822] [INFO] Task succeeded: fastANI
[2024-01-24 12:44:32,823] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:44:32,823] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:44:32,837] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:44:32,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:44:32,838] [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
Blautia massiliensis	strain=GD9	GCA_001487165.1	1737424	1737424	type	True	97.8334	992	1159	95	conclusive
Blautia wexlerae	strain=DSM 19850	GCA_000484655.1	418240	418240	suspected-type	True	82.3076	430	1159	95	below_threshold
Blautia wexlerae	strain=DSM 19850	GCA_025148125.1	418240	418240	suspected-type	True	82.2646	446	1159	95	below_threshold
Blautia intestinalis	strain=27-44	GCA_014297355.1	2763028	2763028	type	True	81.7738	346	1159	95	below_threshold
Mediterraneibacter butyricigenes	strain=KCTC 15684	GCA_003574295.1	2316025	2316025	type	True	81.7384	138	1159	95	below_threshold
Blautia luti	strain=DSM 14534	GCA_009707925.1	89014	89014	suspected-type	True	81.6735	410	1159	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_000153905.1	40520	40520	type	True	81.6624	360	1159	95	below_threshold
Blautia obeum	strain=ATCC 29174	GCA_025147765.1	40520	40520	type	True	81.6225	359	1159	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	81.4302	133	1159	95	below_threshold
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	81.4123	282	1159	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	81.0457	133	1159	95	below_threshold
Jingyaoa shaoxingensis	strain=NSJ-46	GCA_014385005.1	2763671	2763671	type	True	80.3283	173	1159	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.1817	123	1159	95	below_threshold
Roseburia faecis	strain=M72	GCA_001406815.1	301302	301302	type	True	78.6051	101	1159	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.4221	101	1159	95	below_threshold
Acetatifactor muris	strain=DSM 23669	GCA_024623325.1	879566	879566	type	True	77.2667	50	1159	95	below_threshold
Ruminococcus gauvreauii	strain=DSM 19829	GCA_025151995.1	438033	438033	type	True	76.8102	67	1159	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:44:32,840] [INFO] DFAST Taxonomy check result was written to GCF_020686995.1_ASM2068699v1_genomic.fna/tc_result.tsv
[2024-01-24 12:44:32,840] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:44:32,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:44:32,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/checkm_data
[2024-01-24 12:44:32,842] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:44:32,878] [INFO] Task started: CheckM
[2024-01-24 12:44:32,878] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020686995.1_ASM2068699v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020686995.1_ASM2068699v1_genomic.fna/checkm_input GCF_020686995.1_ASM2068699v1_genomic.fna/checkm_result
[2024-01-24 12:45:05,662] [INFO] Task succeeded: CheckM
[2024-01-24 12:45:05,664] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:45:05,686] [INFO] ===== Completeness check finished =====
[2024-01-24 12:45:05,686] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:45:05,687] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020686995.1_ASM2068699v1_genomic.fna/markers.fasta)
[2024-01-24 12:45:05,687] [INFO] Task started: Blastn
[2024-01-24 12:45:05,687] [INFO] Running command: blastn -query GCF_020686995.1_ASM2068699v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c3510ce-7234-48d1-9187-3d2986d797ac/dqc_reference/reference_markers_gtdb.fasta -out GCF_020686995.1_ASM2068699v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:06,739] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:06,742] [INFO] Selected 7 target genomes.
[2024-01-24 12:45:06,742] [INFO] Target genome list was writen to GCF_020686995.1_ASM2068699v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:45:06,752] [INFO] Task started: fastANI
[2024-01-24 12:45:06,752] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e16101-e05b-4322-b5e2-30b1e44c5a63/GCF_020686995.1_ASM2068699v1_genomic.fna.gz --refList GCF_020686995.1_ASM2068699v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020686995.1_ASM2068699v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:45:12,286] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:12,293] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:45:12,293] [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_001487165.1	s__Blautia_A massiliensis	97.8099	993	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	97.95	95.87	0.85	0.71	55	conclusive
GCA_900751995.1	s__Blautia_A sp900751995	94.6161	462	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	95.05	95.05	0.55	0.55	2	-
GCF_013304735.1	s__Blautia_A sp900066205	90.7516	850	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.18	96.89	0.89	0.81	11	-
GCF_003461955.1	s__Blautia_A sp900066335	90.3955	849	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.91	98.25	0.89	0.82	13	-
GCF_013304825.1	s__Blautia_A schinkii	88.562	826	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	99.24	98.34	0.93	0.82	9	-
GCF_003474435.1	s__Blautia_A sp003474435	88.5619	791	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	98.79	98.21	0.92	0.87	5	-
GCA_900764225.1	s__Blautia_A sp900764225	86.1557	521	1159	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Blautia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:45:12,295] [INFO] GTDB search result was written to GCF_020686995.1_ASM2068699v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:45:12,296] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:45:12,300] [INFO] DFAST_QC result json was written to GCF_020686995.1_ASM2068699v1_genomic.fna/dqc_result.json
[2024-01-24 12:45:12,300] [INFO] DFAST_QC completed!
[2024-01-24 12:45:12,300] [INFO] Total running time: 0h1m1s