[2024-01-25 18:15:20,789] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:15:20,791] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:15:20,791] [INFO] DQC Reference Directory: /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference
[2024-01-25 18:15:21,928] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:15:21,929] [INFO] Task started: Prodigal
[2024-01-25 18:15:21,929] [INFO] Running command: gunzip -c /var/lib/cwl/stgccf39fa7-9ada-46a7-8bb7-10ed8cba7130/GCF_002287235.1_ASM228723v1_genomic.fna.gz | prodigal -d GCF_002287235.1_ASM228723v1_genomic.fna/cds.fna -a GCF_002287235.1_ASM228723v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:15:29,753] [INFO] Task succeeded: Prodigal
[2024-01-25 18:15:29,753] [INFO] Task started: HMMsearch
[2024-01-25 18:15:29,753] [INFO] Running command: hmmsearch --tblout GCF_002287235.1_ASM228723v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/reference_markers.hmm GCF_002287235.1_ASM228723v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:15:29,975] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:15:29,976] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgccf39fa7-9ada-46a7-8bb7-10ed8cba7130/GCF_002287235.1_ASM228723v1_genomic.fna.gz]
[2024-01-25 18:15:30,009] [INFO] Query marker FASTA was written to GCF_002287235.1_ASM228723v1_genomic.fna/markers.fasta
[2024-01-25 18:15:30,010] [INFO] Task started: Blastn
[2024-01-25 18:15:30,010] [INFO] Running command: blastn -query GCF_002287235.1_ASM228723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/reference_markers.fasta -out GCF_002287235.1_ASM228723v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:15:30,451] [INFO] Task succeeded: Blastn
[2024-01-25 18:15:30,454] [INFO] Selected 6 target genomes.
[2024-01-25 18:15:30,455] [INFO] Target genome list was writen to GCF_002287235.1_ASM228723v1_genomic.fna/target_genomes.txt
[2024-01-25 18:15:30,460] [INFO] Task started: fastANI
[2024-01-25 18:15:30,460] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf39fa7-9ada-46a7-8bb7-10ed8cba7130/GCF_002287235.1_ASM228723v1_genomic.fna.gz --refList GCF_002287235.1_ASM228723v1_genomic.fna/target_genomes.txt --output GCF_002287235.1_ASM228723v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:15:39,196] [INFO] Task succeeded: fastANI
[2024-01-25 18:15:39,196] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:15:39,197] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:15:39,202] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:15:39,203] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:15:39,203] [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 spelaei	strain=MC-15	GCA_002287235.1	1036679	1036679	type	True	100.0	1459	1475	95	conclusive
Methanosarcina vacuolata	strain=Z-761	GCA_000969905.1	2215	2215	type	True	86.8878	1064	1475	95	below_threshold
Methanosarcina barkeri	strain=MS	GCA_000970025.1	2208	2208	type	True	86.6775	1093	1475	95	below_threshold
Methanosarcina barkeri	strain=JCM 10043	GCA_001316305.1	2208	2208	type	True	86.6608	1024	1475	95	below_threshold
Methanosarcina flavescens	strain=E03.2	GCA_001304615.2	1715806	1715806	type	True	81.0634	704	1475	95	below_threshold
Methanosarcina thermophila	strain=TM-1	GCA_000969885.1	2210	2210	type	True	80.5531	695	1475	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:15:39,204] [INFO] DFAST Taxonomy check result was written to GCF_002287235.1_ASM228723v1_genomic.fna/tc_result.tsv
[2024-01-25 18:15:39,204] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:15:39,205] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:15:39,205] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/checkm_data
[2024-01-25 18:15:39,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:15:39,255] [INFO] Task started: CheckM
[2024-01-25 18:15:39,256] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002287235.1_ASM228723v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002287235.1_ASM228723v1_genomic.fna/checkm_input GCF_002287235.1_ASM228723v1_genomic.fna/checkm_result
[2024-01-25 18:16:08,042] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:08,043] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:08,068] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:08,068] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:08,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002287235.1_ASM228723v1_genomic.fna/markers.fasta)
[2024-01-25 18:16:08,069] [INFO] Task started: Blastn
[2024-01-25 18:16:08,069] [INFO] Running command: blastn -query GCF_002287235.1_ASM228723v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd6af346d-764d-4159-ba8c-b386d6f715d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002287235.1_ASM228723v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:08,582] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:08,586] [INFO] Selected 6 target genomes.
[2024-01-25 18:16:08,587] [INFO] Target genome list was writen to GCF_002287235.1_ASM228723v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:08,595] [INFO] Task started: fastANI
[2024-01-25 18:16:08,595] [INFO] Running command: fastANI --query /var/lib/cwl/stgccf39fa7-9ada-46a7-8bb7-10ed8cba7130/GCF_002287235.1_ASM228723v1_genomic.fna.gz --refList GCF_002287235.1_ASM228723v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002287235.1_ASM228723v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:18,308] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:18,313] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:18,314] [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_002287235.1	s__Methanosarcina spelaei	100.0	1459	1475	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	95.12	95.12	0.84	0.84	2	conclusive
GCF_000970305.1	s__Methanosarcina barkeri_A	94.5459	1236	1475	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	93.4977	1061	1475	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969905.1	s__Methanosarcina vacuolata	86.8781	1064	1475	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.34	98.34	0.91	0.91	2	-
GCA_002505485.1	s__Methanosarcina sp002505485	86.2865	894	1475	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	84.0935	879	1475	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	97.74	97.33	0.90	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:18,315] [INFO] GTDB search result was written to GCF_002287235.1_ASM228723v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:18,315] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:18,318] [INFO] DFAST_QC result json was written to GCF_002287235.1_ASM228723v1_genomic.fna/dqc_result.json
[2024-01-25 18:16:18,319] [INFO] DFAST_QC completed!
[2024-01-25 18:16:18,319] [INFO] Total running time: 0h0m58s