[2024-01-24 13:21:55,990] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:55,992] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:55,992] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference
[2024-01-24 13:21:57,305] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:57,306] [INFO] Task started: Prodigal
[2024-01-24 13:21:57,306] [INFO] Running command: gunzip -c /var/lib/cwl/stg28c1bdda-852c-4b09-afe0-c81c5819fa1b/GCF_000970085.1_ASM97008v1_genomic.fna.gz | prodigal -d GCF_000970085.1_ASM97008v1_genomic.fna/cds.fna -a GCF_000970085.1_ASM97008v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,694] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,694] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,695] [INFO] Running command: hmmsearch --tblout GCF_000970085.1_ASM97008v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/reference_markers.hmm GCF_000970085.1_ASM97008v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:09,021] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:09,023] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg28c1bdda-852c-4b09-afe0-c81c5819fa1b/GCF_000970085.1_ASM97008v1_genomic.fna.gz]
[2024-01-24 13:22:09,073] [INFO] Query marker FASTA was written to GCF_000970085.1_ASM97008v1_genomic.fna/markers.fasta
[2024-01-24 13:22:09,074] [INFO] Task started: Blastn
[2024-01-24 13:22:09,074] [INFO] Running command: blastn -query GCF_000970085.1_ASM97008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/reference_markers.fasta -out GCF_000970085.1_ASM97008v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:09,641] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:09,646] [INFO] Selected 6 target genomes.
[2024-01-24 13:22:09,646] [INFO] Target genome list was writen to GCF_000970085.1_ASM97008v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:09,654] [INFO] Task started: fastANI
[2024-01-24 13:22:09,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c1bdda-852c-4b09-afe0-c81c5819fa1b/GCF_000970085.1_ASM97008v1_genomic.fna.gz --refList GCF_000970085.1_ASM97008v1_genomic.fna/target_genomes.txt --output GCF_000970085.1_ASM97008v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:17,875] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:17,876] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:17,876] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:17,888] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:17,888] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:17,888] [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 siciliae	strain=T4/M	GCA_000970085.1	38027	38027	type	True	100.0	1670	1672	95	conclusive
Methanosarcina acetivorans	strain=C2A	GCA_000007345.1	2214	2214	type	True	91.6404	1376	1672	95	below_threshold
Methanosarcina horonobensis	strain=HB-1	GCA_000970285.1	418008	418008	type	True	82.2291	992	1672	95	below_threshold
Methanosarcina mazei	strain=S-6	GCA_000970205.1	2209	2209	suspected-type	True	81.2659	852	1672	95	below_threshold
Methanosarcina vacuolata	strain=Z-761	GCA_000969905.1	2215	2215	type	True	79.2836	578	1672	95	below_threshold
Methanosarcina thermophila	strain=TM-1	GCA_000969885.1	2210	2210	type	True	78.5996	414	1672	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:17,890] [INFO] DFAST Taxonomy check result was written to GCF_000970085.1_ASM97008v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:17,890] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:17,891] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:17,891] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/checkm_data
[2024-01-24 13:22:17,893] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:17,954] [INFO] Task started: CheckM
[2024-01-24 13:22:17,955] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000970085.1_ASM97008v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000970085.1_ASM97008v1_genomic.fna/checkm_input GCF_000970085.1_ASM97008v1_genomic.fna/checkm_result
[2024-01-24 13:22:56,035] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:56,036] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:56,059] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:56,059] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:56,060] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000970085.1_ASM97008v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:56,060] [INFO] Task started: Blastn
[2024-01-24 13:22:56,060] [INFO] Running command: blastn -query GCF_000970085.1_ASM97008v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d3a0326-feab-4215-a2d5-1723d42f38ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_000970085.1_ASM97008v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:56,771] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:56,775] [INFO] Selected 5 target genomes.
[2024-01-24 13:22:56,775] [INFO] Target genome list was writen to GCF_000970085.1_ASM97008v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:56,785] [INFO] Task started: fastANI
[2024-01-24 13:22:56,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg28c1bdda-852c-4b09-afe0-c81c5819fa1b/GCF_000970085.1_ASM97008v1_genomic.fna.gz --refList GCF_000970085.1_ASM97008v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000970085.1_ASM97008v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:04,511] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:04,520] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:04,521] [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_000970085.1	s__Methanosarcina siciliae	100.0	1670	1672	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.67	98.18	0.92	0.90	3	conclusive
GCF_000007345.1	s__Methanosarcina acetivorans	91.6158	1378	1672	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.98	99.98	1.00	1.00	2	-
GCF_000969965.1	s__Methanosarcina sp000969965	84.2775	1011	1672	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	99.47	99.47	0.94	0.94	2	-
GCF_000979455.1	s__Methanosarcina sp000979455	84.2399	1003	1672	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanosarcina	95.0	98.06	95.85	0.93	0.85	7	-
GCF_000970265.1	s__Methanosarcina lacustris	83.4012	923	1672	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 13:23:04,523] [INFO] GTDB search result was written to GCF_000970085.1_ASM97008v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:04,523] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:04,528] [INFO] DFAST_QC result json was written to GCF_000970085.1_ASM97008v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:04,529] [INFO] DFAST_QC completed!
[2024-01-24 13:23:04,529] [INFO] Total running time: 0h1m9s