[2024-01-24 13:22:31,224] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:31,228] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:31,229] [INFO] DQC Reference Directory: /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference
[2024-01-24 13:22:32,474] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:32,474] [INFO] Task started: Prodigal
[2024-01-24 13:22:32,475] [INFO] Running command: gunzip -c /var/lib/cwl/stg56e957d0-62d6-4dce-bb69-6801494f05b3/GCF_009830285.1_ASM983028v1_genomic.fna.gz | prodigal -d GCF_009830285.1_ASM983028v1_genomic.fna/cds.fna -a GCF_009830285.1_ASM983028v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:47,105] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:47,106] [INFO] Task started: HMMsearch
[2024-01-24 13:22:47,106] [INFO] Running command: hmmsearch --tblout GCF_009830285.1_ASM983028v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/reference_markers.hmm GCF_009830285.1_ASM983028v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:47,460] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:47,462] [INFO] Found 6/6 markers.
[2024-01-24 13:22:47,517] [INFO] Query marker FASTA was written to GCF_009830285.1_ASM983028v1_genomic.fna/markers.fasta
[2024-01-24 13:22:47,518] [INFO] Task started: Blastn
[2024-01-24 13:22:47,518] [INFO] Running command: blastn -query GCF_009830285.1_ASM983028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/reference_markers.fasta -out GCF_009830285.1_ASM983028v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:48,156] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:48,160] [INFO] Selected 25 target genomes.
[2024-01-24 13:22:48,161] [INFO] Target genome list was writen to GCF_009830285.1_ASM983028v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:48,346] [INFO] Task started: fastANI
[2024-01-24 13:22:48,347] [INFO] Running command: fastANI --query /var/lib/cwl/stg56e957d0-62d6-4dce-bb69-6801494f05b3/GCF_009830285.1_ASM983028v1_genomic.fna.gz --refList GCF_009830285.1_ASM983028v1_genomic.fna/target_genomes.txt --output GCF_009830285.1_ASM983028v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:23:04,140] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:04,140] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:23:04,141] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:23:04,159] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:23:04,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:23:04,160] [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
Sporofaciens musculi	strain=WCA-9-b2	GCA_009830285.1	2681861	2681861	type	True	100.0	1918	1919	95	conclusive
Blautia caecimuris	strain=DSM 29492	GCA_024622975.1	1796615	1796615	type	True	82.759	121	1919	95	below_threshold
Wansuia hejianensis	strain=NSJ-29	GCA_014337215.1	2763667	2763667	type	True	81.7462	66	1919	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_002222595.2	1322	1322	type	True	80.6428	70	1919	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_025152275.1	33038	33038	type	True	80.3599	105	1919	95	below_threshold
Blautia hansenii	strain=DSM 20583	GCA_000156675.1	1322	1322	type	True	80.0843	68	1919	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_002959615.1	33038	33038	suspected-type	True	79.8909	120	1919	95	below_threshold
[Ruminococcus] gnavus	strain=JCM6515	GCA_008121495.1	33038	33038	suspected-type	True	79.792	118	1919	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_004295125.1	29347	29347	suspected-type	True	79.6426	253	1919	95	below_threshold
[Clostridium] scindens	strain=ATCC 35704	GCA_000154505.1	29347	29347	suspected-type	True	79.3194	254	1919	95	below_threshold
[Ruminococcus] gnavus	strain=ATCC 29149	GCA_000169475.1	33038	33038	suspected-type	True	79.1907	116	1919	95	below_threshold
Faecalimonas umbilicata	strain=EGH7	GCA_003402615.1	1912855	1912855	type	True	78.9654	93	1919	95	below_threshold
Bariatricus massiliensis	strain=AT12	GCA_900086725.1	1745713	1745713	type	True	78.7384	127	1919	95	below_threshold
Massilistercora timonensis	strain=Marseille-P3756	GCA_900312975.1	2086584	2086584	type	True	78.5707	168	1919	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_025150085.1	88431	88431	type	True	78.4917	148	1919	95	below_threshold
Dorea longicatena	strain=DSM 13814	GCA_000154065.1	88431	88431	type	True	78.312	146	1919	95	below_threshold
Dorea phocaeensis	strain=Marseille-P4003	GCA_900240315.1	2040291	2040291	type	True	78.0334	163	1919	95	below_threshold
Faecalimonas umbilicata	strain=DSM 103426	GCA_004346095.1	1912855	1912855	type	True	77.9988	87	1919	95	below_threshold
[Clostridium] hylemonae	strain=DSM 15053	GCA_000156515.1	89153	89153	type	True	77.8996	138	1919	95	below_threshold
Merdimonas faecis	strain=BR31	GCA_001754075.1	1653435	1653435	type	True	77.7497	212	1919	95	below_threshold
Hungatella effluvii	strain=DSM 24995	GCA_003201875.1	1096246	1096246	type	True	77.6453	65	1919	95	below_threshold
Mediterraneibacter catenae	strain=SW178	GCA_008691045.1	2594882	2594882	type	True	77.2888	86	1919	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	76.9184	54	1919	95	below_threshold
Diplocloster agilis	strain=ASD5720	GCA_019042275.1	2850323	2850323	type	True	76.5836	52	1919	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:23:04,161] [INFO] DFAST Taxonomy check result was written to GCF_009830285.1_ASM983028v1_genomic.fna/tc_result.tsv
[2024-01-24 13:23:04,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:23:04,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:23:04,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/checkm_data
[2024-01-24 13:23:04,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:23:04,222] [INFO] Task started: CheckM
[2024-01-24 13:23:04,223] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009830285.1_ASM983028v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009830285.1_ASM983028v1_genomic.fna/checkm_input GCF_009830285.1_ASM983028v1_genomic.fna/checkm_result
[2024-01-24 13:23:50,726] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:50,728] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:50,753] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:50,753] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:50,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009830285.1_ASM983028v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:50,754] [INFO] Task started: Blastn
[2024-01-24 13:23:50,754] [INFO] Running command: blastn -query GCF_009830285.1_ASM983028v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc6d68d48-6a7b-4180-bfdb-823257c4ec98/dqc_reference/reference_markers_gtdb.fasta -out GCF_009830285.1_ASM983028v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:51,770] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:51,774] [INFO] Selected 7 target genomes.
[2024-01-24 13:23:51,774] [INFO] Target genome list was writen to GCF_009830285.1_ASM983028v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:51,781] [INFO] Task started: fastANI
[2024-01-24 13:23:51,781] [INFO] Running command: fastANI --query /var/lib/cwl/stg56e957d0-62d6-4dce-bb69-6801494f05b3/GCF_009830285.1_ASM983028v1_genomic.fna.gz --refList GCF_009830285.1_ASM983028v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009830285.1_ASM983028v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:59,698] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:59,710] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:59,710] [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_009830285.1	s__Sporofaciens musculi	100.0	1918	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	97.72	97.71	0.87	0.86	3	conclusive
GCA_910584575.1	s__Sporofaciens sp910584575	87.8793	891	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574885.1	s__Sporofaciens sp910574885	84.4304	959	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	99.41	98.81	0.91	0.83	5	-
GCA_910577685.1	s__Sporofaciens sp910577685	82.8839	699	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011960625.1	s__Sporofaciens sp011960625	82.5791	390	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910587575.1	s__Sporofaciens sp910587575	81.7346	650	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579015.1	s__Sporofaciens sp910579015	79.6926	460	1919	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Sporofaciens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:59,712] [INFO] GTDB search result was written to GCF_009830285.1_ASM983028v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:59,712] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:59,717] [INFO] DFAST_QC result json was written to GCF_009830285.1_ASM983028v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:59,717] [INFO] DFAST_QC completed!
[2024-01-24 13:23:59,717] [INFO] Total running time: 0h1m28s