[2023-06-28 10:46:31,849] [INFO] DFAST_QC pipeline started.
[2023-06-28 10:46:31,855] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 10:46:31,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference
[2023-06-28 10:46:33,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 10:46:33,433] [INFO] Task started: Prodigal
[2023-06-28 10:46:33,433] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ece7298-a4d0-4a56-8c47-f9e429bdd8ec/GCA_019894885.1_ASM1989488v1_genomic.fna.gz | prodigal -d GCA_019894885.1_ASM1989488v1_genomic.fna/cds.fna -a GCA_019894885.1_ASM1989488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 10:46:38,035] [INFO] Task succeeded: Prodigal
[2023-06-28 10:46:38,035] [INFO] Task started: HMMsearch
[2023-06-28 10:46:38,035] [INFO] Running command: hmmsearch --tblout GCA_019894885.1_ASM1989488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/reference_markers.hmm GCA_019894885.1_ASM1989488v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 10:46:38,231] [INFO] Task succeeded: HMMsearch
[2023-06-28 10:46:38,233] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4ece7298-a4d0-4a56-8c47-f9e429bdd8ec/GCA_019894885.1_ASM1989488v1_genomic.fna.gz]
[2023-06-28 10:46:38,262] [INFO] Query marker FASTA was written to GCA_019894885.1_ASM1989488v1_genomic.fna/markers.fasta
[2023-06-28 10:46:38,263] [INFO] Task started: Blastn
[2023-06-28 10:46:38,263] [INFO] Running command: blastn -query GCA_019894885.1_ASM1989488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/reference_markers.fasta -out GCA_019894885.1_ASM1989488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:46:38,729] [INFO] Task succeeded: Blastn
[2023-06-28 10:46:38,732] [INFO] Selected 2 target genomes.
[2023-06-28 10:46:38,732] [INFO] Target genome list was writen to GCA_019894885.1_ASM1989488v1_genomic.fna/target_genomes.txt
[2023-06-28 10:46:38,733] [INFO] Task started: fastANI
[2023-06-28 10:46:38,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ece7298-a4d0-4a56-8c47-f9e429bdd8ec/GCA_019894885.1_ASM1989488v1_genomic.fna.gz --refList GCA_019894885.1_ASM1989488v1_genomic.fna/target_genomes.txt --output GCA_019894885.1_ASM1989488v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 10:46:39,558] [INFO] Task succeeded: fastANI
[2023-06-28 10:46:39,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 10:46:39,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 10:46:39,560] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 10:46:39,560] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 10:46:39,560] [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
--------------------------------------------------------------------------------
[2023-06-28 10:46:39,563] [INFO] DFAST Taxonomy check result was written to GCA_019894885.1_ASM1989488v1_genomic.fna/tc_result.tsv
[2023-06-28 10:46:39,564] [INFO] ===== Taxonomy check completed =====
[2023-06-28 10:46:39,564] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 10:46:39,564] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/checkm_data
[2023-06-28 10:46:39,566] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 10:46:39,597] [INFO] Task started: CheckM
[2023-06-28 10:46:39,597] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_019894885.1_ASM1989488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_019894885.1_ASM1989488v1_genomic.fna/checkm_input GCA_019894885.1_ASM1989488v1_genomic.fna/checkm_result
[2023-06-28 10:47:00,979] [INFO] Task succeeded: CheckM
[2023-06-28 10:47:00,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.47%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 10:47:00,999] [INFO] ===== Completeness check finished =====
[2023-06-28 10:47:00,999] [INFO] ===== Start GTDB Search =====
[2023-06-28 10:47:01,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_019894885.1_ASM1989488v1_genomic.fna/markers.fasta)
[2023-06-28 10:47:01,000] [INFO] Task started: Blastn
[2023-06-28 10:47:01,000] [INFO] Running command: blastn -query GCA_019894885.1_ASM1989488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg237789ee-98d1-4689-81d8-d1668dea5f0f/dqc_reference/reference_markers_gtdb.fasta -out GCA_019894885.1_ASM1989488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 10:47:01,392] [INFO] Task succeeded: Blastn
[2023-06-28 10:47:01,396] [INFO] Selected 6 target genomes.
[2023-06-28 10:47:01,396] [INFO] Target genome list was writen to GCA_019894885.1_ASM1989488v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 10:47:01,401] [INFO] Task started: fastANI
[2023-06-28 10:47:01,401] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ece7298-a4d0-4a56-8c47-f9e429bdd8ec/GCA_019894885.1_ASM1989488v1_genomic.fna.gz --refList GCA_019894885.1_ASM1989488v1_genomic.fna/target_genomes_gtdb.txt --output GCA_019894885.1_ASM1989488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 10:47:05,335] [INFO] Task succeeded: fastANI
[2023-06-28 10:47:05,341] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 10:47:05,342] [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_004375715.1	s__SOKP01 sp004375715	86.25	501	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019057735.1	s__SOKP01 sp019057735	86.191	417	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016839745.1	s__SOKP01 sp016839745	80.7927	472	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013375495.1	s__SOKP01 sp013375495	80.44	527	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013375475.1	s__SOKP01 sp013375475	80.0135	449	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011364925.1	s__SOKP01 sp011364925	76.8648	285	938	d__Archaea;p__Asgardarchaeota;c__Lokiarchaeia;o__CR-4;f__SOKP01;g__SOKP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 10:47:05,343] [INFO] GTDB search result was written to GCA_019894885.1_ASM1989488v1_genomic.fna/result_gtdb.tsv
[2023-06-28 10:47:05,343] [INFO] ===== GTDB Search completed =====
[2023-06-28 10:47:05,346] [INFO] DFAST_QC result json was written to GCA_019894885.1_ASM1989488v1_genomic.fna/dqc_result.json
[2023-06-28 10:47:05,346] [INFO] DFAST_QC completed!
[2023-06-28 10:47:05,346] [INFO] Total running time: 0h0m33s