[2024-01-24 13:41:25,892] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:25,907] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:25,907] [INFO] DQC Reference Directory: /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference
[2024-01-24 13:41:27,386] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,387] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg364af782-f049-43c3-88c4-7278df0b1300/GCF_003722055.1_ASM372205v1_genomic.fna.gz | prodigal -d GCF_003722055.1_ASM372205v1_genomic.fna/cds.fna -a GCF_003722055.1_ASM372205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:32,929] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:32,930] [INFO] Task started: HMMsearch
[2024-01-24 13:41:32,930] [INFO] Running command: hmmsearch --tblout GCF_003722055.1_ASM372205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/reference_markers.hmm GCF_003722055.1_ASM372205v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:33,227] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:33,228] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg364af782-f049-43c3-88c4-7278df0b1300/GCF_003722055.1_ASM372205v1_genomic.fna.gz]
[2024-01-24 13:41:33,257] [INFO] Query marker FASTA was written to GCF_003722055.1_ASM372205v1_genomic.fna/markers.fasta
[2024-01-24 13:41:33,257] [INFO] Task started: Blastn
[2024-01-24 13:41:33,257] [INFO] Running command: blastn -query GCF_003722055.1_ASM372205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/reference_markers.fasta -out GCF_003722055.1_ASM372205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:33,815] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:33,818] [INFO] Selected 7 target genomes.
[2024-01-24 13:41:33,818] [INFO] Target genome list was writen to GCF_003722055.1_ASM372205v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:33,821] [INFO] Task started: fastANI
[2024-01-24 13:41:33,821] [INFO] Running command: fastANI --query /var/lib/cwl/stg364af782-f049-43c3-88c4-7278df0b1300/GCF_003722055.1_ASM372205v1_genomic.fna.gz --refList GCF_003722055.1_ASM372205v1_genomic.fna/target_genomes.txt --output GCF_003722055.1_ASM372205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:37,327] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:37,327] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:37,327] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:37,337] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:41:37,337] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:37,338] [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
Methanohalophilus halophilus	strain=DSM 3094	GCA_003722055.1	2177	2177	type	True	100.0	668	669	95	conclusive
Methanohalophilus halophilus	strain=Z-7982	GCA_001889405.1	2177	2177	type	True	99.9991	669	669	95	conclusive
Methanohalophilus halophilus	strain=Z-7982	GCA_900106905.1	2177	2177	type	True	99.9905	662	669	95	conclusive
Methanohalophilus portucalensis	strain=FDF-1	GCA_900177455.1	39664	39664	type	True	92.8213	578	669	95	below_threshold
Methanohalophilus portucalensis	strain=DSM 7471	GCA_003722115.1	39664	39664	type	True	92.7536	576	669	95	below_threshold
Methanohalophilus profundi	strain=SLHTYRO	GCA_004137855.1	2138083	2138083	type	True	92.612	530	669	95	below_threshold
Methanohalophilus mahii	strain=DSM 5219	GCA_000025865.1	2176	2176	type	True	91.4662	586	669	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:37,341] [INFO] DFAST Taxonomy check result was written to GCF_003722055.1_ASM372205v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:37,341] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:37,342] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:37,342] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/checkm_data
[2024-01-24 13:41:37,343] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:37,377] [INFO] Task started: CheckM
[2024-01-24 13:41:37,377] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003722055.1_ASM372205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003722055.1_ASM372205v1_genomic.fna/checkm_input GCF_003722055.1_ASM372205v1_genomic.fna/checkm_result
[2024-01-24 13:42:01,131] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:01,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:01,155] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:01,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:01,156] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003722055.1_ASM372205v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:01,157] [INFO] Task started: Blastn
[2024-01-24 13:42:01,157] [INFO] Running command: blastn -query GCF_003722055.1_ASM372205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg85364831-a8f6-44e6-8bb5-3c7bc040ca96/dqc_reference/reference_markers_gtdb.fasta -out GCF_003722055.1_ASM372205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:01,612] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:01,616] [INFO] Selected 6 target genomes.
[2024-01-24 13:42:01,616] [INFO] Target genome list was writen to GCF_003722055.1_ASM372205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:01,617] [INFO] Task started: fastANI
[2024-01-24 13:42:01,617] [INFO] Running command: fastANI --query /var/lib/cwl/stg364af782-f049-43c3-88c4-7278df0b1300/GCF_003722055.1_ASM372205v1_genomic.fna.gz --refList GCF_003722055.1_ASM372205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003722055.1_ASM372205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:04,519] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:04,526] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:04,526] [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_001889405.1	s__Methanohalophilus halophilus	99.9991	669	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCF_002761295.1	s__Methanohalophilus portucalensis	92.735	587	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	100.00	100.00	1.00	1.00	4	-
GCF_004137855.1	s__Methanohalophilus profundi	92.6133	529	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215215.1	s__Methanohalophilus euhalobius	92.1029	517	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	99.01	98.21	0.93	0.87	10	-
GCF_003722075.1	s__Methanohalophilus sp003722075	92.0296	539	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025865.1	s__Methanohalophilus mahii	91.4662	586	669	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanosarcinaceae;g__Methanohalophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:04,528] [INFO] GTDB search result was written to GCF_003722055.1_ASM372205v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:04,529] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:04,532] [INFO] DFAST_QC result json was written to GCF_003722055.1_ASM372205v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:04,532] [INFO] DFAST_QC completed!
[2024-01-24 13:42:04,533] [INFO] Total running time: 0h0m39s