[2024-01-25 18:53:50,741] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:50,746] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:50,746] [INFO] DQC Reference Directory: /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference
[2024-01-25 18:53:51,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:51,915] [INFO] Task started: Prodigal
[2024-01-25 18:53:51,915] [INFO] Running command: gunzip -c /var/lib/cwl/stgc97b03ba-4777-4037-a96c-5d31a388d8b7/GCF_017873415.1_ASM1787341v1_genomic.fna.gz | prodigal -d GCF_017873415.1_ASM1787341v1_genomic.fna/cds.fna -a GCF_017873415.1_ASM1787341v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:58,372] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:58,372] [INFO] Task started: HMMsearch
[2024-01-25 18:53:58,372] [INFO] Running command: hmmsearch --tblout GCF_017873415.1_ASM1787341v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/reference_markers.hmm GCF_017873415.1_ASM1787341v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:58,624] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:58,625] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc97b03ba-4777-4037-a96c-5d31a388d8b7/GCF_017873415.1_ASM1787341v1_genomic.fna.gz]
[2024-01-25 18:53:58,652] [INFO] Query marker FASTA was written to GCF_017873415.1_ASM1787341v1_genomic.fna/markers.fasta
[2024-01-25 18:53:58,653] [INFO] Task started: Blastn
[2024-01-25 18:53:58,653] [INFO] Running command: blastn -query GCF_017873415.1_ASM1787341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/reference_markers.fasta -out GCF_017873415.1_ASM1787341v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:59,129] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:59,142] [INFO] Selected 6 target genomes.
[2024-01-25 18:53:59,143] [INFO] Target genome list was writen to GCF_017873415.1_ASM1787341v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:59,154] [INFO] Task started: fastANI
[2024-01-25 18:53:59,154] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97b03ba-4777-4037-a96c-5d31a388d8b7/GCF_017873415.1_ASM1787341v1_genomic.fna.gz --refList GCF_017873415.1_ASM1787341v1_genomic.fna/target_genomes.txt --output GCF_017873415.1_ASM1787341v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:54:03,287] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:03,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:54:03,287] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:54:03,294] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:54:03,294] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:54:03,294] [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 bombayensis	strain=DSM 7082	GCA_017873415.1	38023	38023	type	True	100.0	1019	1023	95	conclusive
Methanolobus tindarius	strain=DSM 2278	GCA_000504205.1	2221	2221	type	True	83.9359	688	1023	95	below_threshold
Methanolobus vulcani	strain=PL 12/M	GCA_900100715.1	38026	38026	type	True	83.8829	707	1023	95	below_threshold
Methanolobus profundi	strain=Mob M	GCA_900114835.1	487685	487685	type	True	80.4803	491	1023	95	below_threshold
Methanolobus psychrotolerans	strain=YSF-03	GCA_002243045.1	1874706	1874706	type	True	79.3062	447	1023	95	below_threshold
Methanococcoides vulcani		GCA_900773955.1	1353158	1353158	type	True	76.9289	84	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:54:03,296] [INFO] DFAST Taxonomy check result was written to GCF_017873415.1_ASM1787341v1_genomic.fna/tc_result.tsv
[2024-01-25 18:54:03,296] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:54:03,297] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:54:03,297] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/checkm_data
[2024-01-25 18:54:03,298] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:54:03,330] [INFO] Task started: CheckM
[2024-01-25 18:54:03,330] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017873415.1_ASM1787341v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017873415.1_ASM1787341v1_genomic.fna/checkm_input GCF_017873415.1_ASM1787341v1_genomic.fna/checkm_result
[2024-01-25 18:54:27,441] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:27,443] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:27,461] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:27,461] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:27,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017873415.1_ASM1787341v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:27,462] [INFO] Task started: Blastn
[2024-01-25 18:54:27,462] [INFO] Running command: blastn -query GCF_017873415.1_ASM1787341v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3783df22-b60d-4061-8d3c-1c390f00ed6d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017873415.1_ASM1787341v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:27,881] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:27,884] [INFO] Selected 6 target genomes.
[2024-01-25 18:54:27,884] [INFO] Target genome list was writen to GCF_017873415.1_ASM1787341v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:27,891] [INFO] Task started: fastANI
[2024-01-25 18:54:27,891] [INFO] Running command: fastANI --query /var/lib/cwl/stgc97b03ba-4777-4037-a96c-5d31a388d8b7/GCF_017873415.1_ASM1787341v1_genomic.fna.gz --refList GCF_017873415.1_ASM1787341v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017873415.1_ASM1787341v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:32,175] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:32,180] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:32,181] [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_017873415.1	s__Methanolobus bombayensis	100.0	1019	1023	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000504205.1	s__Methanolobus tindarius	83.9354	687	1023	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100715.1	s__Methanolobus vulcani	83.8854	705	1023	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	83.651	664	1023	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	80.4677	491	1023	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002507205.1	s__Methanolobus sp002507205	79.6205	395	1023	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanolobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:32,182] [INFO] GTDB search result was written to GCF_017873415.1_ASM1787341v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:32,183] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:32,185] [INFO] DFAST_QC result json was written to GCF_017873415.1_ASM1787341v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:32,185] [INFO] DFAST_QC completed!
[2024-01-25 18:54:32,185] [INFO] Total running time: 0h0m41s