[2024-01-24 13:49:25,360] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:25,362] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:25,362] [INFO] DQC Reference Directory: /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference
[2024-01-24 13:49:26,601] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:26,602] [INFO] Task started: Prodigal
[2024-01-24 13:49:26,602] [INFO] Running command: gunzip -c /var/lib/cwl/stgcff315c4-264d-4662-bb0a-b0d701c7458e/GCF_000970205.1_ASM97020v1_genomic.fna.gz | prodigal -d GCF_000970205.1_ASM97020v1_genomic.fna/cds.fna -a GCF_000970205.1_ASM97020v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:35,529] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:35,530] [INFO] Task started: HMMsearch
[2024-01-24 13:49:35,530] [INFO] Running command: hmmsearch --tblout GCF_000970205.1_ASM97020v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/reference_markers.hmm GCF_000970205.1_ASM97020v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:35,763] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:35,764] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgcff315c4-264d-4662-bb0a-b0d701c7458e/GCF_000970205.1_ASM97020v1_genomic.fna.gz]
[2024-01-24 13:49:35,793] [INFO] Query marker FASTA was written to GCF_000970205.1_ASM97020v1_genomic.fna/markers.fasta
[2024-01-24 13:49:35,794] [INFO] Task started: Blastn
[2024-01-24 13:49:35,794] [INFO] Running command: blastn -query GCF_000970205.1_ASM97020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/reference_markers.fasta -out GCF_000970205.1_ASM97020v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:36,272] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:36,276] [INFO] Selected 6 target genomes.
[2024-01-24 13:49:36,276] [INFO] Target genome list was writen to GCF_000970205.1_ASM97020v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:36,287] [INFO] Task started: fastANI
[2024-01-24 13:49:36,287] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff315c4-264d-4662-bb0a-b0d701c7458e/GCF_000970205.1_ASM97020v1_genomic.fna.gz --refList GCF_000970205.1_ASM97020v1_genomic.fna/target_genomes.txt --output GCF_000970205.1_ASM97020v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:44,724] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:44,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:44,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:44,733] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:44,733] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:44,733] [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 mazei	strain=S-6	GCA_000970205.1	2209	2209	suspected-type	True	100.0	1380	1380	95	conclusive
Methanosarcina horonobensis	strain=HB-1	GCA_000970285.1	418008	418008	type	True	83.2093	948	1380	95	below_threshold
Methanosarcina acetivorans	strain=C2A	GCA_000007345.1	2214	2214	type	True	81.422	857	1380	95	below_threshold
Methanosarcina siciliae	strain=T4/M	GCA_000970085.1	38027	38027	type	True	81.41	831	1380	95	below_threshold
Methanosarcina vacuolata	strain=Z-761	GCA_000969905.1	2215	2215	type	True	79.0904	524	1380	95	below_threshold
Methanosarcina spelaei	strain=MC-15	GCA_002287235.1	1036679	1036679	type	True	78.6763	513	1380	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:44,735] [INFO] DFAST Taxonomy check result was written to GCF_000970205.1_ASM97020v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:44,742] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:44,742] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:44,743] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/checkm_data
[2024-01-24 13:49:44,744] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:44,789] [INFO] Task started: CheckM
[2024-01-24 13:49:44,789] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970205.1_ASM97020v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970205.1_ASM97020v1_genomic.fna/checkm_input GCF_000970205.1_ASM97020v1_genomic.fna/checkm_result
[2024-01-24 13:50:17,414] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:17,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:17,436] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:17,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970205.1_ASM97020v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:17,437] [INFO] Task started: Blastn
[2024-01-24 13:50:17,437] [INFO] Running command: blastn -query GCF_000970205.1_ASM97020v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9d6484f0-4ead-4d5e-a836-d978a3e7f860/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970205.1_ASM97020v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:17,940] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:17,943] [INFO] Selected 7 target genomes.
[2024-01-24 13:50:17,944] [INFO] Target genome list was writen to GCF_000970205.1_ASM97020v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:17,950] [INFO] Task started: fastANI
[2024-01-24 13:50:17,951] [INFO] Running command: fastANI --query /var/lib/cwl/stgcff315c4-264d-4662-bb0a-b0d701c7458e/GCF_000970205.1_ASM97020v1_genomic.fna.gz --refList GCF_000970205.1_ASM97020v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000970205.1_ASM97020v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:25,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:25,244] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:25,244] [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_000970205.1	s__Methanosarcina mazei	100.0	1380	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.56	98.01	0.92	0.88	73	conclusive
GCA_013331265.1	s__Methanosarcina sp10923u	83.4496	733	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970285.1	s__Methanosarcina horonobensis	83.2225	949	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.79	99.79	1.00	1.00	2	-
GCF_000979455.1	s__Methanosarcina sp000979455	81.6642	844	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.06	95.85	0.93	0.85	7	-
GCF_000969965.1	s__Methanosarcina sp000969965	81.2535	814	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.47	99.47	0.94	0.94	2	-
GCF_000970265.1	s__Methanosarcina lacustris	81.036	802	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017883485.1	s__Methanosarcina sp017883485	77.9812	284	1380	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:25,249] [INFO] GTDB search result was written to GCF_000970205.1_ASM97020v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:25,249] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:25,253] [INFO] DFAST_QC result json was written to GCF_000970205.1_ASM97020v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:25,253] [INFO] DFAST_QC completed!
[2024-01-24 13:50:25,254] [INFO] Total running time: 0h0m60s