[2024-01-25 19:55:35,954] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:35,956] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:35,956] [INFO] DQC Reference Directory: /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference
[2024-01-25 19:55:37,177] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:37,179] [INFO] Task started: Prodigal
[2024-01-25 19:55:37,179] [INFO] Running command: gunzip -c /var/lib/cwl/stg3bcb25a0-4874-4c6c-ae23-6f92b639f99a/GCF_000968535.2_ASM96853v1_genomic.fna.gz | prodigal -d GCF_000968535.2_ASM96853v1_genomic.fna/cds.fna -a GCF_000968535.2_ASM96853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:48,632] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:48,632] [INFO] Task started: HMMsearch
[2024-01-25 19:55:48,632] [INFO] Running command: hmmsearch --tblout GCF_000968535.2_ASM96853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/reference_markers.hmm GCF_000968535.2_ASM96853v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:48,979] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:48,980] [INFO] Found 6/6 markers.
[2024-01-25 19:55:49,017] [INFO] Query marker FASTA was written to GCF_000968535.2_ASM96853v1_genomic.fna/markers.fasta
[2024-01-25 19:55:49,017] [INFO] Task started: Blastn
[2024-01-25 19:55:49,018] [INFO] Running command: blastn -query GCF_000968535.2_ASM96853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/reference_markers.fasta -out GCF_000968535.2_ASM96853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:49,664] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:49,667] [INFO] Selected 22 target genomes.
[2024-01-25 19:55:49,667] [INFO] Target genome list was writen to GCF_000968535.2_ASM96853v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:49,688] [INFO] Task started: fastANI
[2024-01-25 19:55:49,688] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bcb25a0-4874-4c6c-ae23-6f92b639f99a/GCF_000968535.2_ASM96853v1_genomic.fna.gz --refList GCF_000968535.2_ASM96853v1_genomic.fna/target_genomes.txt --output GCF_000968535.2_ASM96853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:56:17,914] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:17,915] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:56:17,916] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:56:17,925] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:56:17,925] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:56:17,925] [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
Methylotuvimicrobium alcaliphilum	strain=20Z	GCA_000968535.1	271065	271065	type	True	100.0	1598	1598	95	conclusive
Methylovulum miyakonense	strain=HT12	GCA_000384075.1	645578	645578	type	True	77.3453	86	1598	95	below_threshold
Methylosarcina fibrata	strain=AML-C10	GCA_000372865.1	105972	105972	type	True	77.2975	145	1598	95	below_threshold
Methylobacter marinus	strain=A45	GCA_000383855.1	34058	34058	type	True	77.2189	175	1598	95	below_threshold
Methylomarinum vadi	strain=IT-4	GCA_000733935.1	438855	438855	type	True	77.056	164	1598	95	below_threshold
Methylomonas albis	strain=EbA	GCA_014850955.1	1854563	1854563	type	True	76.9888	100	1598	95	below_threshold
Methylobacter tundripaludum	strain=SV96	GCA_000190755.3	173365	173365	type	True	76.7788	163	1598	95	below_threshold
Methylomonas denitrificans	strain=FJG1	GCA_000785705.2	1538553	1538553	type	True	76.7164	143	1598	95	below_threshold
Methylomonas koyamae	strain=Fw12E-Y	GCA_019669905.1	702114	702114	suspected-type	True	76.5082	138	1598	95	below_threshold
Crenothrix polyspora		GCA_900163755.1	360316	360316	reftype	True	76.231	54	1598	95	below_threshold
Methylomonas koyamae	strain=JCM 16701	GCA_001312005.1	702114	702114	suspected-type	True	76.1339	123	1598	95	below_threshold
Methyloglobulus morosus	strain=KoM1	GCA_000496735.2	1410681	1410681	type	True	75.8623	54	1598	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:56:17,926] [INFO] DFAST Taxonomy check result was written to GCF_000968535.2_ASM96853v1_genomic.fna/tc_result.tsv
[2024-01-25 19:56:17,927] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:56:17,927] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:56:17,927] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/checkm_data
[2024-01-25 19:56:17,928] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:56:17,972] [INFO] Task started: CheckM
[2024-01-25 19:56:17,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000968535.2_ASM96853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000968535.2_ASM96853v1_genomic.fna/checkm_input GCF_000968535.2_ASM96853v1_genomic.fna/checkm_result
[2024-01-25 19:56:54,415] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:54,416] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:54,444] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:54,444] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:54,446] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000968535.2_ASM96853v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:54,446] [INFO] Task started: Blastn
[2024-01-25 19:56:54,446] [INFO] Running command: blastn -query GCF_000968535.2_ASM96853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgda2063d6-2de5-4075-9500-3e56b3356370/dqc_reference/reference_markers_gtdb.fasta -out GCF_000968535.2_ASM96853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:55,539] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:55,542] [INFO] Selected 7 target genomes.
[2024-01-25 19:56:55,542] [INFO] Target genome list was writen to GCF_000968535.2_ASM96853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:55,570] [INFO] Task started: fastANI
[2024-01-25 19:56:55,570] [INFO] Running command: fastANI --query /var/lib/cwl/stg3bcb25a0-4874-4c6c-ae23-6f92b639f99a/GCF_000968535.2_ASM96853v1_genomic.fna.gz --refList GCF_000968535.2_ASM96853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000968535.2_ASM96853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:57:37,464] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:37,469] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:57:37,470] [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_000968535.2	s__Methylotuvimicrobium alcaliphilum	100.0	1598	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.1408	N/A	N/A	N/A	N/A	1	conclusive
GCF_000341735.1	s__Methylotuvimicrobium buryatense	95.1167	1387	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.1408	99.98	99.98	0.99	0.99	2	-
GCA_018830325.1	s__Methylotuvimicrobium sp018830325	92.5161	1175	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003932755.1	s__Methylotuvimicrobium sp003932755	90.9742	1219	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007135635.1	s__Methylotuvimicrobium sp007135635	88.4857	613	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006788925.1	s__Methylotuvimicrobium kenyense	85.7324	1069	1598	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Methylococcales;f__Methylomonadaceae;g__Methylotuvimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:57:37,473] [INFO] GTDB search result was written to GCF_000968535.2_ASM96853v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:57:37,473] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:57:37,476] [INFO] DFAST_QC result json was written to GCF_000968535.2_ASM96853v1_genomic.fna/dqc_result.json
[2024-01-25 19:57:37,476] [INFO] DFAST_QC completed!
[2024-01-25 19:57:37,476] [INFO] Total running time: 0h2m2s