[2024-01-24 13:50:10,039] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:10,041] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:10,041] [INFO] DQC Reference Directory: /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference
[2024-01-24 13:50:11,328] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,329] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,329] [INFO] Running command: gunzip -c /var/lib/cwl/stg74e1926e-f9f5-4caf-a545-3d06c6c8d628/GCF_002243045.1_ASM224304v1_genomic.fna.gz | prodigal -d GCF_002243045.1_ASM224304v1_genomic.fna/cds.fna -a GCF_002243045.1_ASM224304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:18,909] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:18,909] [INFO] Task started: HMMsearch
[2024-01-24 13:50:18,910] [INFO] Running command: hmmsearch --tblout GCF_002243045.1_ASM224304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/reference_markers.hmm GCF_002243045.1_ASM224304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:19,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:19,185] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg74e1926e-f9f5-4caf-a545-3d06c6c8d628/GCF_002243045.1_ASM224304v1_genomic.fna.gz]
[2024-01-24 13:50:19,216] [INFO] Query marker FASTA was written to GCF_002243045.1_ASM224304v1_genomic.fna/markers.fasta
[2024-01-24 13:50:19,216] [INFO] Task started: Blastn
[2024-01-24 13:50:19,216] [INFO] Running command: blastn -query GCF_002243045.1_ASM224304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/reference_markers.fasta -out GCF_002243045.1_ASM224304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:19,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:19,725] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:19,726] [INFO] Target genome list was writen to GCF_002243045.1_ASM224304v1_genomic.fna/target_genomes.txt
[2024-01-24 13:50:19,730] [INFO] Task started: fastANI
[2024-01-24 13:50:19,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e1926e-f9f5-4caf-a545-3d06c6c8d628/GCF_002243045.1_ASM224304v1_genomic.fna.gz --refList GCF_002243045.1_ASM224304v1_genomic.fna/target_genomes.txt --output GCF_002243045.1_ASM224304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:23,509] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:23,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:23,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:23,519] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:23,520] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:23,520] [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
Methanolobus psychrotolerans	strain=YSF-03	GCA_002243045.1	1874706	1874706	type	True	100.0	1001	1004	95	conclusive
Methanolobus vulcani	strain=PL 12/M	GCA_900100715.1	38026	38026	type	True	79.7735	420	1004	95	below_threshold
Methanolobus profundi	strain=Mob M	GCA_900114835.1	487685	487685	type	True	79.7276	462	1004	95	below_threshold
Methanolobus bombayensis	strain=DSM 7082	GCA_017873415.1	38023	38023	type	True	79.4486	433	1004	95	below_threshold
Methanolobus tindarius	strain=DSM 2278	GCA_000504205.1	2221	2221	type	True	79.313	435	1004	95	below_threshold
Methanolobus halotolerans	strain=SY-01	GCA_004745425.1	2052935	2052935	type	True	77.9177	197	1004	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:23,522] [INFO] DFAST Taxonomy check result was written to GCF_002243045.1_ASM224304v1_genomic.fna/tc_result.tsv
[2024-01-24 13:50:23,522] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:23,522] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:23,522] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/checkm_data
[2024-01-24 13:50:23,523] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:23,553] [INFO] Task started: CheckM
[2024-01-24 13:50:23,554] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002243045.1_ASM224304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002243045.1_ASM224304v1_genomic.fna/checkm_input GCF_002243045.1_ASM224304v1_genomic.fna/checkm_result
[2024-01-24 13:50:51,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:51,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:51,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:51,576] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:51,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002243045.1_ASM224304v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:51,577] [INFO] Task started: Blastn
[2024-01-24 13:50:51,577] [INFO] Running command: blastn -query GCF_002243045.1_ASM224304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg403d2d8d-db39-4b5f-b94e-1ddf965f2d90/dqc_reference/reference_markers_gtdb.fasta -out GCF_002243045.1_ASM224304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:52,022] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:52,026] [INFO] Selected 6 target genomes.
[2024-01-24 13:50:52,027] [INFO] Target genome list was writen to GCF_002243045.1_ASM224304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:52,034] [INFO] Task started: fastANI
[2024-01-24 13:50:52,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg74e1926e-f9f5-4caf-a545-3d06c6c8d628/GCF_002243045.1_ASM224304v1_genomic.fna.gz --refList GCF_002243045.1_ASM224304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002243045.1_ASM224304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:55,956] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:55,968] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:55,968] [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_002243045.1	s__Methanolobus psychrotolerans	100.0	1001	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002507205.1	s__Methanolobus sp002507205	82.8089	544	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016278385.1	s__Methanolobus sp016278385	81.248	553	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114835.1	s__Methanolobus profundi	79.7333	463	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006546655.1	s__Methanolobus vulcani_A	79.6489	415	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000504205.1	s__Methanolobus tindarius	79.3072	436	1004	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:55,970] [INFO] GTDB search result was written to GCF_002243045.1_ASM224304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:55,970] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:55,974] [INFO] DFAST_QC result json was written to GCF_002243045.1_ASM224304v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:55,974] [INFO] DFAST_QC completed!
[2024-01-24 13:50:55,974] [INFO] Total running time: 0h0m46s