[2023-06-17 18:33:36,174] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:33:36,177] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:33:36,177] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference
[2023-06-17 18:33:38,173] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:33:38,175] [INFO] Task started: Prodigal
[2023-06-17 18:33:38,175] [INFO] Running command: gunzip -c /var/lib/cwl/stg13fceeb9-15ce-4db5-a2a0-06e6ca691941/GCA_013335585.1_ASM1333558v1_genomic.fna.gz | prodigal -d GCA_013335585.1_ASM1333558v1_genomic.fna/cds.fna -a GCA_013335585.1_ASM1333558v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:33:40,207] [INFO] Task succeeded: Prodigal
[2023-06-17 18:33:40,207] [INFO] Task started: HMMsearch
[2023-06-17 18:33:40,208] [INFO] Running command: hmmsearch --tblout GCA_013335585.1_ASM1333558v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/reference_markers.hmm GCA_013335585.1_ASM1333558v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:33:40,415] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:33:40,417] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg13fceeb9-15ce-4db5-a2a0-06e6ca691941/GCA_013335585.1_ASM1333558v1_genomic.fna.gz]
[2023-06-17 18:33:40,437] [INFO] Query marker FASTA was written to GCA_013335585.1_ASM1333558v1_genomic.fna/markers.fasta
[2023-06-17 18:33:40,438] [INFO] Task started: Blastn
[2023-06-17 18:33:40,438] [INFO] Running command: blastn -query GCA_013335585.1_ASM1333558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/reference_markers.fasta -out GCA_013335585.1_ASM1333558v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:33:42,325] [INFO] Task succeeded: Blastn
[2023-06-17 18:33:42,329] [INFO] Selected 6 target genomes.
[2023-06-17 18:33:42,330] [INFO] Target genome list was writen to GCA_013335585.1_ASM1333558v1_genomic.fna/target_genomes.txt
[2023-06-17 18:33:42,377] [INFO] Task started: fastANI
[2023-06-17 18:33:42,378] [INFO] Running command: fastANI --query /var/lib/cwl/stg13fceeb9-15ce-4db5-a2a0-06e6ca691941/GCA_013335585.1_ASM1333558v1_genomic.fna.gz --refList GCA_013335585.1_ASM1333558v1_genomic.fna/target_genomes.txt --output GCA_013335585.1_ASM1333558v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:33:45,278] [INFO] Task succeeded: fastANI
[2023-06-17 18:33:45,279] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:33:45,279] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:33:45,281] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:33:45,281] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 18:33:45,281] [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
--------------------------------------------------------------------------------
[2023-06-17 18:33:45,284] [INFO] DFAST Taxonomy check result was written to GCA_013335585.1_ASM1333558v1_genomic.fna/tc_result.tsv
[2023-06-17 18:33:45,285] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:33:45,285] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:33:45,285] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/checkm_data
[2023-06-17 18:33:45,290] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:33:45,306] [INFO] Task started: CheckM
[2023-06-17 18:33:45,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013335585.1_ASM1333558v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013335585.1_ASM1333558v1_genomic.fna/checkm_input GCA_013335585.1_ASM1333558v1_genomic.fna/checkm_result
[2023-06-17 18:34:01,310] [INFO] Task succeeded: CheckM
[2023-06-17 18:34:01,312] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.81%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 18:34:01,335] [INFO] ===== Completeness check finished =====
[2023-06-17 18:34:01,336] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:34:01,336] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013335585.1_ASM1333558v1_genomic.fna/markers.fasta)
[2023-06-17 18:34:01,336] [INFO] Task started: Blastn
[2023-06-17 18:34:01,336] [INFO] Running command: blastn -query GCA_013335585.1_ASM1333558v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d6b54c1-4d82-4850-b2b3-b5f0f5df5b46/dqc_reference/reference_markers_gtdb.fasta -out GCA_013335585.1_ASM1333558v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:34:01,970] [INFO] Task succeeded: Blastn
[2023-06-17 18:34:01,975] [INFO] Selected 7 target genomes.
[2023-06-17 18:34:01,975] [INFO] Target genome list was writen to GCA_013335585.1_ASM1333558v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:34:01,980] [INFO] Task started: fastANI
[2023-06-17 18:34:01,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg13fceeb9-15ce-4db5-a2a0-06e6ca691941/GCA_013335585.1_ASM1333558v1_genomic.fna.gz --refList GCA_013335585.1_ASM1333558v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013335585.1_ASM1333558v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:34:04,819] [INFO] Task succeeded: fastANI
[2023-06-17 18:34:04,826] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:34:04,827] [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_002256595.1	s__Methanothrix sp002256595	97.1788	114	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	98.21	98.21	0.89	0.89	2	conclusive
GCA_002505805.1	s__Methanothrix sp002505805	83.9913	107	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	96.80	96.80	0.74	0.74	2	-
GCA_016927055.1	s__Methanothrix sp016927055	79.7377	80	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204415.1	s__Methanothrix soehngenii	79.0471	67	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	98.33	96.33	0.94	0.87	11	-
GCA_002067705.1	s__Methanothrix sp002067705	79.0019	66	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871465.1	s__Methanothrix sp903871465	78.5722	60	129	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanotrichales;f__Methanotrichaceae;g__Methanothrix	95.0	99.90	99.77	0.96	0.93	9	-
--------------------------------------------------------------------------------
[2023-06-17 18:34:04,829] [INFO] GTDB search result was written to GCA_013335585.1_ASM1333558v1_genomic.fna/result_gtdb.tsv
[2023-06-17 18:34:04,829] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:34:04,832] [INFO] DFAST_QC result json was written to GCA_013335585.1_ASM1333558v1_genomic.fna/dqc_result.json
[2023-06-17 18:34:04,832] [INFO] DFAST_QC completed!
[2023-06-17 18:34:04,832] [INFO] Total running time: 0h0m29s