[2024-01-25 18:10:36,021] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:10:36,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:10:36,023] [INFO] DQC Reference Directory: /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference
[2024-01-25 18:10:37,201] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:10:37,202] [INFO] Task started: Prodigal
[2024-01-25 18:10:37,202] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0018ee5-5644-490c-b867-c10a9551973a/GCF_001541255.1_ASM154125v1_genomic.fna.gz | prodigal -d GCF_001541255.1_ASM154125v1_genomic.fna/cds.fna -a GCF_001541255.1_ASM154125v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:10:44,154] [INFO] Task succeeded: Prodigal
[2024-01-25 18:10:44,154] [INFO] Task started: HMMsearch
[2024-01-25 18:10:44,154] [INFO] Running command: hmmsearch --tblout GCF_001541255.1_ASM154125v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/reference_markers.hmm GCF_001541255.1_ASM154125v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:10:44,368] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:10:44,369] [INFO] Found 6/6 markers.
[2024-01-25 18:10:44,401] [INFO] Query marker FASTA was written to GCF_001541255.1_ASM154125v1_genomic.fna/markers.fasta
[2024-01-25 18:10:44,401] [INFO] Task started: Blastn
[2024-01-25 18:10:44,401] [INFO] Running command: blastn -query GCF_001541255.1_ASM154125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/reference_markers.fasta -out GCF_001541255.1_ASM154125v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:44,927] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:44,930] [INFO] Selected 14 target genomes.
[2024-01-25 18:10:44,930] [INFO] Target genome list was writen to GCF_001541255.1_ASM154125v1_genomic.fna/target_genomes.txt
[2024-01-25 18:10:44,938] [INFO] Task started: fastANI
[2024-01-25 18:10:44,938] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0018ee5-5644-490c-b867-c10a9551973a/GCF_001541255.1_ASM154125v1_genomic.fna.gz --refList GCF_001541255.1_ASM154125v1_genomic.fna/target_genomes.txt --output GCF_001541255.1_ASM154125v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:10:51,605] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:51,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:10:51,606] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:10:51,607] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:10:51,607] [INFO] The taxonomy check result is classified as 'no_hit'.
[2024-01-25 18:10:51,607] [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
--------------------------------------------------------------------------------
[2024-01-25 18:10:51,612] [INFO] DFAST Taxonomy check result was written to GCF_001541255.1_ASM154125v1_genomic.fna/tc_result.tsv
[2024-01-25 18:10:51,612] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:10:51,613] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:10:51,613] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/checkm_data
[2024-01-25 18:10:51,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:10:51,652] [INFO] Task started: CheckM
[2024-01-25 18:10:51,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001541255.1_ASM154125v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001541255.1_ASM154125v1_genomic.fna/checkm_input GCF_001541255.1_ASM154125v1_genomic.fna/checkm_result
[2024-01-25 18:11:16,698] [INFO] Task succeeded: CheckM
[2024-01-25 18:11:16,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:11:16,717] [INFO] ===== Completeness check finished =====
[2024-01-25 18:11:16,718] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:11:16,718] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001541255.1_ASM154125v1_genomic.fna/markers.fasta)
[2024-01-25 18:11:16,718] [INFO] Task started: Blastn
[2024-01-25 18:11:16,718] [INFO] Running command: blastn -query GCF_001541255.1_ASM154125v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge76642d9-bea1-41bc-a586-d4a589771415/dqc_reference/reference_markers_gtdb.fasta -out GCF_001541255.1_ASM154125v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:11:17,541] [INFO] Task succeeded: Blastn
[2024-01-25 18:11:17,543] [INFO] Selected 8 target genomes.
[2024-01-25 18:11:17,544] [INFO] Target genome list was writen to GCF_001541255.1_ASM154125v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:11:17,550] [INFO] Task started: fastANI
[2024-01-25 18:11:17,550] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0018ee5-5644-490c-b867-c10a9551973a/GCF_001541255.1_ASM154125v1_genomic.fna.gz --refList GCF_001541255.1_ASM154125v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001541255.1_ASM154125v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:11:22,779] [INFO] Task succeeded: fastANI
[2024-01-25 18:11:22,784] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:11:22,785] [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
GCA_001541255.1	s__HCH-1 sp001541255	100.0	1122	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	99.98	99.96	0.98	0.97	3	conclusive
GCA_015233485.1	s__HCH-1 sp015233485	80.718	525	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015233685.1	s__HCH-1 sp015233685	80.4835	401	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015233015.1	s__HCH-1 sp015233015	80.3741	663	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015233265.1	s__HCH-1 sp015233265	80.1414	409	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015233045.1	s__HCH-1 sp015233045	79.7967	478	1126	d__Bacteria;p__Nitrospirota;c__Thermodesulfovibrionia;o__Thermodesulfovibrionales;f__Magnetobacteriaceae;g__HCH-1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:11:22,786] [INFO] GTDB search result was written to GCF_001541255.1_ASM154125v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:11:22,786] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:11:22,788] [INFO] DFAST_QC result json was written to GCF_001541255.1_ASM154125v1_genomic.fna/dqc_result.json
[2024-01-25 18:11:22,788] [INFO] DFAST_QC completed!
[2024-01-25 18:11:22,788] [INFO] Total running time: 0h0m47s