[2023-06-27 06:26:19,633] [INFO] DFAST_QC pipeline started.
[2023-06-27 06:26:19,640] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 06:26:19,640] [INFO] DQC Reference Directory: /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference
[2023-06-27 06:26:21,731] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 06:26:21,732] [INFO] Task started: Prodigal
[2023-06-27 06:26:21,732] [INFO] Running command: gunzip -c /var/lib/cwl/stga5219a1f-fc88-4075-a659-c1dd00a8a45e/GCA_002495565.1_ASM249556v1_genomic.fna.gz | prodigal -d GCA_002495565.1_ASM249556v1_genomic.fna/cds.fna -a GCA_002495565.1_ASM249556v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 06:26:27,584] [INFO] Task succeeded: Prodigal
[2023-06-27 06:26:27,585] [INFO] Task started: HMMsearch
[2023-06-27 06:26:27,585] [INFO] Running command: hmmsearch --tblout GCA_002495565.1_ASM249556v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/reference_markers.hmm GCA_002495565.1_ASM249556v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 06:26:27,770] [INFO] Task succeeded: HMMsearch
[2023-06-27 06:26:27,771] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga5219a1f-fc88-4075-a659-c1dd00a8a45e/GCA_002495565.1_ASM249556v1_genomic.fna.gz]
[2023-06-27 06:26:28,013] [INFO] Query marker FASTA was written to GCA_002495565.1_ASM249556v1_genomic.fna/markers.fasta
[2023-06-27 06:26:28,013] [INFO] Task started: Blastn
[2023-06-27 06:26:28,013] [INFO] Running command: blastn -query GCA_002495565.1_ASM249556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/reference_markers.fasta -out GCA_002495565.1_ASM249556v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:26:28,714] [INFO] Task succeeded: Blastn
[2023-06-27 06:26:28,717] [INFO] Selected 6 target genomes.
[2023-06-27 06:26:28,717] [INFO] Target genome list was writen to GCA_002495565.1_ASM249556v1_genomic.fna/target_genomes.txt
[2023-06-27 06:26:28,719] [INFO] Task started: fastANI
[2023-06-27 06:26:28,719] [INFO] Running command: fastANI --query /var/lib/cwl/stga5219a1f-fc88-4075-a659-c1dd00a8a45e/GCA_002495565.1_ASM249556v1_genomic.fna.gz --refList GCA_002495565.1_ASM249556v1_genomic.fna/target_genomes.txt --output GCA_002495565.1_ASM249556v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 06:26:34,069] [INFO] Task succeeded: fastANI
[2023-06-27 06:26:34,069] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 06:26:34,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 06:26:34,077] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 06:26:34,077] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 06:26:34,077] [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 flavescens	strain=E03.2	GCA_001304615.2	1715806	1715806	type	True	82.0278	699	1001	95	below_threshold
Methanosarcina vacuolata	strain=Z-761	GCA_000969905.1	2215	2215	type	True	81.932	710	1001	95	below_threshold
Methanosarcina barkeri	strain=JCM 10043	GCA_001316305.1	2208	2208	type	True	81.7343	692	1001	95	below_threshold
Methanosarcina spelaei	strain=MC-15	GCA_002287235.1	1036679	1036679	type	True	81.7334	690	1001	95	below_threshold
Methanosarcina barkeri	strain=MS	GCA_000970025.1	2208	2208	type	True	81.683	733	1001	95	below_threshold
Methanosarcina thermophila	strain=TM-1	GCA_000969885.1	2210	2210	type	True	81.3594	648	1001	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 06:26:34,079] [INFO] DFAST Taxonomy check result was written to GCA_002495565.1_ASM249556v1_genomic.fna/tc_result.tsv
[2023-06-27 06:26:34,080] [INFO] ===== Taxonomy check completed =====
[2023-06-27 06:26:34,080] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 06:26:34,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/checkm_data
[2023-06-27 06:26:34,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 06:26:34,114] [INFO] Task started: CheckM
[2023-06-27 06:26:34,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002495565.1_ASM249556v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002495565.1_ASM249556v1_genomic.fna/checkm_input GCA_002495565.1_ASM249556v1_genomic.fna/checkm_result
[2023-06-27 06:26:56,971] [INFO] Task succeeded: CheckM
[2023-06-27 06:26:56,972] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 06:26:56,988] [INFO] ===== Completeness check finished =====
[2023-06-27 06:26:56,988] [INFO] ===== Start GTDB Search =====
[2023-06-27 06:26:56,989] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002495565.1_ASM249556v1_genomic.fna/markers.fasta)
[2023-06-27 06:26:56,989] [INFO] Task started: Blastn
[2023-06-27 06:26:56,989] [INFO] Running command: blastn -query GCA_002495565.1_ASM249556v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg05fc1527-50cb-4610-97cd-e698f0187a99/dqc_reference/reference_markers_gtdb.fasta -out GCA_002495565.1_ASM249556v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 06:26:57,406] [INFO] Task succeeded: Blastn
[2023-06-27 06:26:57,421] [INFO] Selected 8 target genomes.
[2023-06-27 06:26:57,421] [INFO] Target genome list was writen to GCA_002495565.1_ASM249556v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 06:26:57,425] [INFO] Task started: fastANI
[2023-06-27 06:26:57,425] [INFO] Running command: fastANI --query /var/lib/cwl/stga5219a1f-fc88-4075-a659-c1dd00a8a45e/GCA_002495565.1_ASM249556v1_genomic.fna.gz --refList GCA_002495565.1_ASM249556v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002495565.1_ASM249556v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 06:27:04,278] [INFO] Task succeeded: fastANI
[2023-06-27 06:27:04,286] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 06:27:04,287] [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
GCA_002499445.1	s__Methanosarcina sp002499445	99.4533	922	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.41	96.88	0.92	0.88	16	conclusive
GCA_002509325.1	s__Methanosarcina sp002509325	89.5046	682	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.58	99.58	0.85	0.85	2	-
GCA_002496565.1	s__Methanosarcina sp002496565	82.854	751	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	97.74	97.33	0.90	0.88	3	-
GCA_002505485.1	s__Methanosarcina sp002505485	82.4701	701	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000195895.1	s__Methanosarcina barkeri_B	81.9518	722	1001	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	81.9419	709	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.34	98.34	0.91	0.91	2	-
GCA_013331275.1	s__Methanosarcina sp11020u	81.4315	647	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969885.1	s__Methanosarcina thermophila	81.346	650	1001	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.75	99.68	0.97	0.95	9	-
--------------------------------------------------------------------------------
[2023-06-27 06:27:04,296] [INFO] GTDB search result was written to GCA_002495565.1_ASM249556v1_genomic.fna/result_gtdb.tsv
[2023-06-27 06:27:04,296] [INFO] ===== GTDB Search completed =====
[2023-06-27 06:27:04,303] [INFO] DFAST_QC result json was written to GCA_002495565.1_ASM249556v1_genomic.fna/dqc_result.json
[2023-06-27 06:27:04,303] [INFO] DFAST_QC completed!
[2023-06-27 06:27:04,303] [INFO] Total running time: 0h0m45s