[2024-01-24 12:22:34,349] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:34,351] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:34,352] [INFO] DQC Reference Directory: /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference
[2024-01-24 12:22:35,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:35,790] [INFO] Task started: Prodigal
[2024-01-24 12:22:35,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg121ae4b2-e8f5-4bc2-afae-ef92aea64a7b/GCF_902807005.1_14-2711_R47_genomic.fna.gz | prodigal -d GCF_902807005.1_14-2711_R47_genomic.fna/cds.fna -a GCF_902807005.1_14-2711_R47_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:38,451] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:38,451] [INFO] Task started: HMMsearch
[2024-01-24 12:22:38,451] [INFO] Running command: hmmsearch --tblout GCF_902807005.1_14-2711_R47_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/reference_markers.hmm GCF_902807005.1_14-2711_R47_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:38,655] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:38,656] [INFO] Found 6/6 markers.
[2024-01-24 12:22:38,679] [INFO] Query marker FASTA was written to GCF_902807005.1_14-2711_R47_genomic.fna/markers.fasta
[2024-01-24 12:22:38,680] [INFO] Task started: Blastn
[2024-01-24 12:22:38,680] [INFO] Running command: blastn -query GCF_902807005.1_14-2711_R47_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/reference_markers.fasta -out GCF_902807005.1_14-2711_R47_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:39,300] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:39,303] [INFO] Selected 8 target genomes.
[2024-01-24 12:22:39,304] [INFO] Target genome list was writen to GCF_902807005.1_14-2711_R47_genomic.fna/target_genomes.txt
[2024-01-24 12:22:39,307] [INFO] Task started: fastANI
[2024-01-24 12:22:39,307] [INFO] Running command: fastANI --query /var/lib/cwl/stg121ae4b2-e8f5-4bc2-afae-ef92aea64a7b/GCF_902807005.1_14-2711_R47_genomic.fna.gz --refList GCF_902807005.1_14-2711_R47_genomic.fna/target_genomes.txt --output GCF_902807005.1_14-2711_R47_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:41,788] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:41,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:41,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:41,793] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:41,793] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:41,794] [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
Chlamydiifrater phoenicopteri		GCA_902807005.1	2681469	2681469	type	True	100.0	400	400	95	conclusive
Chlamydiifrater volucris		GCA_902806995.1	2681470	2681470	type	True	79.6745	223	400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:41,795] [INFO] DFAST Taxonomy check result was written to GCF_902807005.1_14-2711_R47_genomic.fna/tc_result.tsv
[2024-01-24 12:22:41,795] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:41,795] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:41,796] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/checkm_data
[2024-01-24 12:22:41,797] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:41,810] [INFO] Task started: CheckM
[2024-01-24 12:22:41,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902807005.1_14-2711_R47_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902807005.1_14-2711_R47_genomic.fna/checkm_input GCF_902807005.1_14-2711_R47_genomic.fna/checkm_result
[2024-01-24 12:22:58,465] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:58,467] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:58,486] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:58,486] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:58,487] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902807005.1_14-2711_R47_genomic.fna/markers.fasta)
[2024-01-24 12:22:58,487] [INFO] Task started: Blastn
[2024-01-24 12:22:58,487] [INFO] Running command: blastn -query GCF_902807005.1_14-2711_R47_genomic.fna/markers.fasta -db /var/lib/cwl/stg86b0e1df-e076-4405-a6f8-74cbb1fdb840/dqc_reference/reference_markers_gtdb.fasta -out GCF_902807005.1_14-2711_R47_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:59,195] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:59,200] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:59,200] [INFO] Target genome list was writen to GCF_902807005.1_14-2711_R47_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:59,205] [INFO] Task started: fastANI
[2024-01-24 12:22:59,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg121ae4b2-e8f5-4bc2-afae-ef92aea64a7b/GCF_902807005.1_14-2711_R47_genomic.fna.gz --refList GCF_902807005.1_14-2711_R47_genomic.fna/target_genomes_gtdb.txt --output GCF_902807005.1_14-2711_R47_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:02,176] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:02,179] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:02,179] [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
GCF_902807005.1	s__Chlamydiifrater phoenicopteri	100.0	400	400	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydiifrater	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_902806995.1	s__Chlamydiifrater volucris	79.6614	222	400	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydiifrater	95.0	99.60	99.60	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:02,181] [INFO] GTDB search result was written to GCF_902807005.1_14-2711_R47_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:02,182] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:02,186] [INFO] DFAST_QC result json was written to GCF_902807005.1_14-2711_R47_genomic.fna/dqc_result.json
[2024-01-24 12:23:02,186] [INFO] DFAST_QC completed!
[2024-01-24 12:23:02,186] [INFO] Total running time: 0h0m28s