[2024-01-24 13:12:53,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:53,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:53,034] [INFO] DQC Reference Directory: /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference
[2024-01-24 13:12:54,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:54,342] [INFO] Task started: Prodigal
[2024-01-24 13:12:54,342] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2c7bf7a-ff46-4ab0-b692-0c42d992ee6e/GCF_000970025.1_ASM97002v1_genomic.fna.gz | prodigal -d GCF_000970025.1_ASM97002v1_genomic.fna/cds.fna -a GCF_000970025.1_ASM97002v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:04,271] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:04,271] [INFO] Task started: HMMsearch
[2024-01-24 13:13:04,272] [INFO] Running command: hmmsearch --tblout GCF_000970025.1_ASM97002v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/reference_markers.hmm GCF_000970025.1_ASM97002v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:04,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:04,663] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc2c7bf7a-ff46-4ab0-b692-0c42d992ee6e/GCF_000970025.1_ASM97002v1_genomic.fna.gz]
[2024-01-24 13:13:04,717] [INFO] Query marker FASTA was written to GCF_000970025.1_ASM97002v1_genomic.fna/markers.fasta
[2024-01-24 13:13:04,718] [INFO] Task started: Blastn
[2024-01-24 13:13:04,718] [INFO] Running command: blastn -query GCF_000970025.1_ASM97002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/reference_markers.fasta -out GCF_000970025.1_ASM97002v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:05,247] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:05,250] [INFO] Selected 6 target genomes.
[2024-01-24 13:13:05,250] [INFO] Target genome list was writen to GCF_000970025.1_ASM97002v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:05,255] [INFO] Task started: fastANI
[2024-01-24 13:13:05,255] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c7bf7a-ff46-4ab0-b692-0c42d992ee6e/GCF_000970025.1_ASM97002v1_genomic.fna.gz --refList GCF_000970025.1_ASM97002v1_genomic.fna/target_genomes.txt --output GCF_000970025.1_ASM97002v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:14,336] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:14,336] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:14,336] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:14,343] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:14,343] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:14,343] [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
Methanosarcina barkeri	strain=MS	GCA_000970025.1	2208	2208	type	True	100.0	1524	1524	95	conclusive
Methanosarcina barkeri	strain=JCM 10043	GCA_001316305.1	2208	2208	type	True	99.7428	1356	1524	95	conclusive
Methanosarcina vacuolata	strain=Z-761	GCA_000969905.1	2215	2215	type	True	90.2218	1155	1524	95	below_threshold
Methanosarcina spelaei	strain=MC-15	GCA_002287235.1	1036679	1036679	type	True	86.6999	1060	1524	95	below_threshold
Methanosarcina flavescens	strain=E03.2	GCA_001304615.2	1715806	1715806	type	True	81.2071	761	1524	95	below_threshold
Methanosarcina thermophila	strain=TM-1	GCA_000969885.1	2210	2210	type	True	81.0957	704	1524	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:14,345] [INFO] DFAST Taxonomy check result was written to GCF_000970025.1_ASM97002v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:14,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:14,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:14,346] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/checkm_data
[2024-01-24 13:13:14,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:14,396] [INFO] Task started: CheckM
[2024-01-24 13:13:14,396] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970025.1_ASM97002v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970025.1_ASM97002v1_genomic.fna/checkm_input GCF_000970025.1_ASM97002v1_genomic.fna/checkm_result
[2024-01-24 13:13:48,679] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:48,680] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:48,703] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:48,704] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:48,704] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970025.1_ASM97002v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:48,705] [INFO] Task started: Blastn
[2024-01-24 13:13:48,705] [INFO] Running command: blastn -query GCF_000970025.1_ASM97002v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb787c723-7327-478a-80ae-6eb72e66926c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970025.1_ASM97002v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:49,136] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:49,140] [INFO] Selected 8 target genomes.
[2024-01-24 13:13:49,140] [INFO] Target genome list was writen to GCF_000970025.1_ASM97002v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:49,151] [INFO] Task started: fastANI
[2024-01-24 13:13:49,152] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2c7bf7a-ff46-4ab0-b692-0c42d992ee6e/GCF_000970025.1_ASM97002v1_genomic.fna.gz --refList GCF_000970025.1_ASM97002v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000970025.1_ASM97002v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:01,359] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:01,374] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:01,374] [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_000970025.1	s__Methanosarcina barkeri	100.0	1524	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.62	99.28	0.97	0.94	5	conclusive
GCF_000195895.1	s__Methanosarcina barkeri_B	91.5006	1231	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969905.1	s__Methanosarcina vacuolata	90.197	1158	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.34	98.34	0.91	0.91	2	-
GCF_002287235.1	s__Methanosarcina spelaei	86.7453	1056	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	95.12	95.12	0.84	0.84	2	-
GCA_002505485.1	s__Methanosarcina sp002505485	86.5469	951	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970305.1	s__Methanosarcina barkeri_A	86.3796	1141	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013331275.1	s__Methanosarcina sp11020u	86.0183	983	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002496565.1	s__Methanosarcina sp002496565	84.395	925	1524	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	97.74	97.33	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:01,377] [INFO] GTDB search result was written to GCF_000970025.1_ASM97002v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:01,378] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:01,382] [INFO] DFAST_QC result json was written to GCF_000970025.1_ASM97002v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:01,382] [INFO] DFAST_QC completed!
[2024-01-24 13:14:01,382] [INFO] Total running time: 0h1m8s