[2023-06-05 00:30:32,263] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:32,267] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:32,267] [INFO] DQC Reference Directory: /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference
[2023-06-05 00:30:33,914] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:33,915] [INFO] Task started: Prodigal
[2023-06-05 00:30:33,915] [INFO] Running command: gunzip -c /var/lib/cwl/stgfd0ff2cb-11a2-47c3-a041-c52b18f3aa20/GCA_010031885.1_ASM1003188v1_genomic.fna.gz | prodigal -d GCA_010031885.1_ASM1003188v1_genomic.fna/cds.fna -a GCA_010031885.1_ASM1003188v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:36,981] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:36,982] [INFO] Task started: HMMsearch
[2023-06-05 00:30:36,982] [INFO] Running command: hmmsearch --tblout GCA_010031885.1_ASM1003188v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/reference_markers.hmm GCA_010031885.1_ASM1003188v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:37,222] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:37,223] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgfd0ff2cb-11a2-47c3-a041-c52b18f3aa20/GCA_010031885.1_ASM1003188v1_genomic.fna.gz]
[2023-06-05 00:30:37,240] [INFO] Query marker FASTA was written to GCA_010031885.1_ASM1003188v1_genomic.fna/markers.fasta
[2023-06-05 00:30:37,240] [INFO] Task started: Blastn
[2023-06-05 00:30:37,240] [INFO] Running command: blastn -query GCA_010031885.1_ASM1003188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/reference_markers.fasta -out GCA_010031885.1_ASM1003188v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:37,829] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:37,833] [INFO] Selected 21 target genomes.
[2023-06-05 00:30:37,834] [INFO] Target genome list was writen to GCA_010031885.1_ASM1003188v1_genomic.fna/target_genomes.txt
[2023-06-05 00:30:37,839] [INFO] Task started: fastANI
[2023-06-05 00:30:37,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0ff2cb-11a2-47c3-a041-c52b18f3aa20/GCA_010031885.1_ASM1003188v1_genomic.fna.gz --refList GCA_010031885.1_ASM1003188v1_genomic.fna/target_genomes.txt --output GCA_010031885.1_ASM1003188v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:49,174] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:49,175] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:49,175] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:49,176] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:49,177] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:30:49,177] [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
--------------------------------------------------------------------------------
[2023-06-05 00:30:49,179] [INFO] DFAST Taxonomy check result was written to GCA_010031885.1_ASM1003188v1_genomic.fna/tc_result.tsv
[2023-06-05 00:30:49,179] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:49,180] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:49,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/checkm_data
[2023-06-05 00:30:49,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:49,206] [INFO] Task started: CheckM
[2023-06-05 00:30:49,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_010031885.1_ASM1003188v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_010031885.1_ASM1003188v1_genomic.fna/checkm_input GCA_010031885.1_ASM1003188v1_genomic.fna/checkm_result
[2023-06-05 00:31:07,033] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:07,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.58%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:31:07,056] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:07,056] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:07,057] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_010031885.1_ASM1003188v1_genomic.fna/markers.fasta)
[2023-06-05 00:31:07,057] [INFO] Task started: Blastn
[2023-06-05 00:31:07,057] [INFO] Running command: blastn -query GCA_010031885.1_ASM1003188v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg383ab05c-6448-4a05-a2a8-fd86d806da96/dqc_reference/reference_markers_gtdb.fasta -out GCA_010031885.1_ASM1003188v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:07,813] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:07,817] [INFO] Selected 18 target genomes.
[2023-06-05 00:31:07,817] [INFO] Target genome list was writen to GCA_010031885.1_ASM1003188v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:08,026] [INFO] Task started: fastANI
[2023-06-05 00:31:08,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgfd0ff2cb-11a2-47c3-a041-c52b18f3aa20/GCA_010031885.1_ASM1003188v1_genomic.fna.gz --refList GCA_010031885.1_ASM1003188v1_genomic.fna/target_genomes_gtdb.txt --output GCA_010031885.1_ASM1003188v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:14,937] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:14,947] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:31:14,947] [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_010031885.1	s__RGXB01 sp010031885	100.0	395	399	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__2-12-FULL-49-11;f__RGXB01;g__RGXB01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016866475.1	s__RGXB01 sp016866475	79.4013	94	399	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__2-12-FULL-49-11;f__RGXB01;g__RGXB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866495.1	s__RGXB01 sp016866495	78.6019	109	399	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__2-12-FULL-49-11;f__RGXB01;g__RGXB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010029555.1	s__RGXB01 sp010029555	78.1493	57	399	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__2-12-FULL-49-11;f__RGXB01;g__RGXB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:31:14,967] [INFO] GTDB search result was written to GCA_010031885.1_ASM1003188v1_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:14,968] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:14,971] [INFO] DFAST_QC result json was written to GCA_010031885.1_ASM1003188v1_genomic.fna/dqc_result.json
[2023-06-05 00:31:14,972] [INFO] DFAST_QC completed!
[2023-06-05 00:31:14,972] [INFO] Total running time: 0h0m43s