[2024-01-25 19:47:20,444] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:47:20,446] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:47:20,446] [INFO] DQC Reference Directory: /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference
[2024-01-25 19:47:21,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:47:21,566] [INFO] Task started: Prodigal
[2024-01-25 19:47:21,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg25821275-6f76-45df-b4be-e02c1b03360d/GCF_017873855.1_ASM1787385v1_genomic.fna.gz | prodigal -d GCF_017873855.1_ASM1787385v1_genomic.fna/cds.fna -a GCF_017873855.1_ASM1787385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:47:28,102] [INFO] Task succeeded: Prodigal
[2024-01-25 19:47:28,103] [INFO] Task started: HMMsearch
[2024-01-25 19:47:28,103] [INFO] Running command: hmmsearch --tblout GCF_017873855.1_ASM1787385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/reference_markers.hmm GCF_017873855.1_ASM1787385v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:47:28,270] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:47:28,271] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg25821275-6f76-45df-b4be-e02c1b03360d/GCF_017873855.1_ASM1787385v1_genomic.fna.gz]
[2024-01-25 19:47:28,296] [INFO] Query marker FASTA was written to GCF_017873855.1_ASM1787385v1_genomic.fna/markers.fasta
[2024-01-25 19:47:28,296] [INFO] Task started: Blastn
[2024-01-25 19:47:28,296] [INFO] Running command: blastn -query GCF_017873855.1_ASM1787385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/reference_markers.fasta -out GCF_017873855.1_ASM1787385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:28,750] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:28,753] [INFO] Selected 6 target genomes.
[2024-01-25 19:47:28,753] [INFO] Target genome list was writen to GCF_017873855.1_ASM1787385v1_genomic.fna/target_genomes.txt
[2024-01-25 19:47:28,757] [INFO] Task started: fastANI
[2024-01-25 19:47:28,757] [INFO] Running command: fastANI --query /var/lib/cwl/stg25821275-6f76-45df-b4be-e02c1b03360d/GCF_017873855.1_ASM1787385v1_genomic.fna.gz --refList GCF_017873855.1_ASM1787385v1_genomic.fna/target_genomes.txt --output GCF_017873855.1_ASM1787385v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:31,678] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:31,678] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:31,679] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:31,684] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:31,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:31,684] [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
Methanolinea mesophila	strain=DSM 23604	GCA_017873855.1	547055	547055	type	True	100.0	887	887	95	conclusive
Methanoculleus bourgensis	strain=MS2T	GCA_000304355.2	83986	83986	type	True	77.1309	66	887	95	below_threshold
Methanoculleus chikugoensis	strain=MG62	GCA_019669965.1	118126	118126	type	True	77.0275	89	887	95	below_threshold
Methanofollis ethanolicus	strain=HASU	GCA_001571385.1	488124	488124	type	True	76.8286	67	887	95	below_threshold
Methanoculleus sediminis	strain=S3Fa	GCA_001017125.1	1550566	1550566	type	True	76.7578	97	887	95	below_threshold
Methanoculleus marisnigri	strain=JR1	GCA_000015825.1	2198	2198	type	True	76.5831	98	887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:31,685] [INFO] DFAST Taxonomy check result was written to GCF_017873855.1_ASM1787385v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:31,686] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:31,686] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:31,686] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/checkm_data
[2024-01-25 19:47:31,687] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:31,713] [INFO] Task started: CheckM
[2024-01-25 19:47:31,713] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873855.1_ASM1787385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873855.1_ASM1787385v1_genomic.fna/checkm_input GCF_017873855.1_ASM1787385v1_genomic.fna/checkm_result
[2024-01-25 19:47:54,981] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:54,982] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:54,996] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:54,996] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:54,996] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873855.1_ASM1787385v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:54,997] [INFO] Task started: Blastn
[2024-01-25 19:47:54,997] [INFO] Running command: blastn -query GCF_017873855.1_ASM1787385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb8eb201b-01ed-43b6-a54b-57ceb0a6fccc/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873855.1_ASM1787385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:55,440] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:55,443] [INFO] Selected 9 target genomes.
[2024-01-25 19:47:55,443] [INFO] Target genome list was writen to GCF_017873855.1_ASM1787385v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:55,450] [INFO] Task started: fastANI
[2024-01-25 19:47:55,450] [INFO] Running command: fastANI --query /var/lib/cwl/stg25821275-6f76-45df-b4be-e02c1b03360d/GCF_017873855.1_ASM1787385v1_genomic.fna.gz --refList GCF_017873855.1_ASM1787385v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873855.1_ASM1787385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:47:59,496] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:59,502] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:47:59,502] [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_017873855.1	s__Methanolinea_B mesophila	100.0	887	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanolinea_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002503825.1	s__UBA467 sp002503825	77.4716	123	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__UBA467	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016699325.1	s__UBA9949 sp016699325	77.2078	99	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__UBA9949	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000304355.2	s__Methanoculleus bourgensis	77.1309	66	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	96.25	95.89	0.90	0.87	7	-
GCA_018263335.1	s__Methanolinea_A sp002067155	76.9205	126	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanolinea_A	95.0	99.35	99.35	0.89	0.89	2	-
GCA_002067095.1	s__Methanolinea_A sp002067095	76.6653	125	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoregulaceae;g__Methanolinea_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841385.1	s__Methanoculleus sp016841385	76.5947	73	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499455.1	s__Methanoculleus sp002499455	76.2892	86	887	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanoculleaceae;g__Methanoculleus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:47:59,504] [INFO] GTDB search result was written to GCF_017873855.1_ASM1787385v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:47:59,504] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:47:59,506] [INFO] DFAST_QC result json was written to GCF_017873855.1_ASM1787385v1_genomic.fna/dqc_result.json
[2024-01-25 19:47:59,506] [INFO] DFAST_QC completed!
[2024-01-25 19:47:59,506] [INFO] Total running time: 0h0m39s