[2023-06-19 04:59:07,687] [INFO] DFAST_QC pipeline started.
[2023-06-19 04:59:07,693] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 04:59:07,694] [INFO] DQC Reference Directory: /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference
[2023-06-19 04:59:08,987] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 04:59:08,988] [INFO] Task started: Prodigal
[2023-06-19 04:59:08,988] [INFO] Running command: gunzip -c /var/lib/cwl/stgee215272-76db-4255-9384-f9519a4e63b8/GCA_014237125.1_ASM1423712v1_genomic.fna.gz | prodigal -d GCA_014237125.1_ASM1423712v1_genomic.fna/cds.fna -a GCA_014237125.1_ASM1423712v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 04:59:14,718] [INFO] Task succeeded: Prodigal
[2023-06-19 04:59:14,718] [INFO] Task started: HMMsearch
[2023-06-19 04:59:14,718] [INFO] Running command: hmmsearch --tblout GCA_014237125.1_ASM1423712v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/reference_markers.hmm GCA_014237125.1_ASM1423712v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 04:59:14,949] [INFO] Task succeeded: HMMsearch
[2023-06-19 04:59:14,953] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgee215272-76db-4255-9384-f9519a4e63b8/GCA_014237125.1_ASM1423712v1_genomic.fna.gz]
[2023-06-19 04:59:14,982] [INFO] Query marker FASTA was written to GCA_014237125.1_ASM1423712v1_genomic.fna/markers.fasta
[2023-06-19 04:59:14,982] [INFO] Task started: Blastn
[2023-06-19 04:59:14,982] [INFO] Running command: blastn -query GCA_014237125.1_ASM1423712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/reference_markers.fasta -out GCA_014237125.1_ASM1423712v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:15,490] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:15,495] [INFO] Selected 7 target genomes.
[2023-06-19 04:59:15,495] [INFO] Target genome list was writen to GCA_014237125.1_ASM1423712v1_genomic.fna/target_genomes.txt
[2023-06-19 04:59:15,497] [INFO] Task started: fastANI
[2023-06-19 04:59:15,498] [INFO] Running command: fastANI --query /var/lib/cwl/stgee215272-76db-4255-9384-f9519a4e63b8/GCA_014237125.1_ASM1423712v1_genomic.fna.gz --refList GCA_014237125.1_ASM1423712v1_genomic.fna/target_genomes.txt --output GCA_014237125.1_ASM1423712v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 04:59:18,598] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:18,599] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 04:59:18,599] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 04:59:18,601] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 04:59:18,601] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 04:59:18,601] [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
--------------------------------------------------------------------------------
[2023-06-19 04:59:18,604] [INFO] DFAST Taxonomy check result was written to GCA_014237125.1_ASM1423712v1_genomic.fna/tc_result.tsv
[2023-06-19 04:59:18,604] [INFO] ===== Taxonomy check completed =====
[2023-06-19 04:59:18,604] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 04:59:18,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/checkm_data
[2023-06-19 04:59:18,609] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 04:59:18,639] [INFO] Task started: CheckM
[2023-06-19 04:59:18,639] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_014237125.1_ASM1423712v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_014237125.1_ASM1423712v1_genomic.fna/checkm_input GCA_014237125.1_ASM1423712v1_genomic.fna/checkm_result
[2023-06-19 04:59:43,100] [INFO] Task succeeded: CheckM
[2023-06-19 04:59:43,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.54%
Contamintation: 5.45%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2023-06-19 04:59:43,132] [INFO] ===== Completeness check finished =====
[2023-06-19 04:59:43,132] [INFO] ===== Start GTDB Search =====
[2023-06-19 04:59:43,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_014237125.1_ASM1423712v1_genomic.fna/markers.fasta)
[2023-06-19 04:59:43,133] [INFO] Task started: Blastn
[2023-06-19 04:59:43,133] [INFO] Running command: blastn -query GCA_014237125.1_ASM1423712v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg35842cfb-0dfc-4a0b-8945-f96dd2d07ef7/dqc_reference/reference_markers_gtdb.fasta -out GCA_014237125.1_ASM1423712v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 04:59:43,603] [INFO] Task succeeded: Blastn
[2023-06-19 04:59:43,608] [INFO] Selected 6 target genomes.
[2023-06-19 04:59:43,609] [INFO] Target genome list was writen to GCA_014237125.1_ASM1423712v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 04:59:43,611] [INFO] Task started: fastANI
[2023-06-19 04:59:43,611] [INFO] Running command: fastANI --query /var/lib/cwl/stgee215272-76db-4255-9384-f9519a4e63b8/GCA_014237125.1_ASM1423712v1_genomic.fna.gz --refList GCA_014237125.1_ASM1423712v1_genomic.fna/target_genomes_gtdb.txt --output GCA_014237125.1_ASM1423712v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 04:59:46,092] [INFO] Task succeeded: fastANI
[2023-06-19 04:59:46,103] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 04:59:46,103] [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_014237145.1	s__Methanocomedens sp014237145	99.6086	562	722	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__Methanocomedens	95.0	99.75	99.61	0.90	0.78	5	conclusive
GCA_009649835.1	s__Methanocomedens sp009649835	92.008	351	722	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__Methanocomedens	95.0	96.64	96.30	0.66	0.59	4	-
GCA_013330355.1	s__Methanocomedens sp7939u	89.7727	243	722	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__Methanocomedens	95.0	97.31	97.31	0.69	0.69	2	-
GCA_013374385.1	s__QBUR01 sp013374385	79.5703	118	722	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__QBUR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859725.1	s__Kmv04 sp014859725	78.1335	122	722	d__Archaea;p__Halobacteriota;c__Methanosarcinia;o__Methanosarcinales;f__Methanocomedenaceae;g__Kmv04	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 04:59:46,106] [INFO] GTDB search result was written to GCA_014237125.1_ASM1423712v1_genomic.fna/result_gtdb.tsv
[2023-06-19 04:59:46,108] [INFO] ===== GTDB Search completed =====
[2023-06-19 04:59:46,112] [INFO] DFAST_QC result json was written to GCA_014237125.1_ASM1423712v1_genomic.fna/dqc_result.json
[2023-06-19 04:59:46,112] [INFO] DFAST_QC completed!
[2023-06-19 04:59:46,113] [INFO] Total running time: 0h0m38s