[2023-06-18 17:51:01,183] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:51:01,191] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:51:01,191] [INFO] DQC Reference Directory: /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference
[2023-06-18 17:51:02,400] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:51:02,400] [INFO] Task started: Prodigal
[2023-06-18 17:51:02,401] [INFO] Running command: gunzip -c /var/lib/cwl/stgae99fb7f-4d0b-4109-a300-c2fcf540a3be/GCA_018664885.1_ASM1866488v1_genomic.fna.gz | prodigal -d GCA_018664885.1_ASM1866488v1_genomic.fna/cds.fna -a GCA_018664885.1_ASM1866488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:51:07,879] [INFO] Task succeeded: Prodigal
[2023-06-18 17:51:07,880] [INFO] Task started: HMMsearch
[2023-06-18 17:51:07,880] [INFO] Running command: hmmsearch --tblout GCA_018664885.1_ASM1866488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/reference_markers.hmm GCA_018664885.1_ASM1866488v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:51:08,097] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:51:08,099] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgae99fb7f-4d0b-4109-a300-c2fcf540a3be/GCA_018664885.1_ASM1866488v1_genomic.fna.gz]
[2023-06-18 17:51:08,121] [INFO] Query marker FASTA was written to GCA_018664885.1_ASM1866488v1_genomic.fna/markers.fasta
[2023-06-18 17:51:08,122] [INFO] Task started: Blastn
[2023-06-18 17:51:08,122] [INFO] Running command: blastn -query GCA_018664885.1_ASM1866488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/reference_markers.fasta -out GCA_018664885.1_ASM1866488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:08,739] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:08,746] [INFO] Selected 15 target genomes.
[2023-06-18 17:51:08,746] [INFO] Target genome list was writen to GCA_018664885.1_ASM1866488v1_genomic.fna/target_genomes.txt
[2023-06-18 17:51:08,749] [INFO] Task started: fastANI
[2023-06-18 17:51:08,749] [INFO] Running command: fastANI --query /var/lib/cwl/stgae99fb7f-4d0b-4109-a300-c2fcf540a3be/GCA_018664885.1_ASM1866488v1_genomic.fna.gz --refList GCA_018664885.1_ASM1866488v1_genomic.fna/target_genomes.txt --output GCA_018664885.1_ASM1866488v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:51:17,010] [INFO] Task succeeded: fastANI
[2023-06-18 17:51:17,010] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:51:17,010] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:51:17,012] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:51:17,012] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 17:51:17,012] [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
--------------------------------------------------------------------------------
[2023-06-18 17:51:17,016] [INFO] DFAST Taxonomy check result was written to GCA_018664885.1_ASM1866488v1_genomic.fna/tc_result.tsv
[2023-06-18 17:51:17,017] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:51:17,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:51:17,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/checkm_data
[2023-06-18 17:51:17,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:51:17,052] [INFO] Task started: CheckM
[2023-06-18 17:51:17,052] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018664885.1_ASM1866488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018664885.1_ASM1866488v1_genomic.fna/checkm_input GCA_018664885.1_ASM1866488v1_genomic.fna/checkm_result
[2023-06-18 17:51:40,552] [INFO] Task succeeded: CheckM
[2023-06-18 17:51:40,554] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-18 17:51:40,575] [INFO] ===== Completeness check finished =====
[2023-06-18 17:51:40,576] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:51:40,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018664885.1_ASM1866488v1_genomic.fna/markers.fasta)
[2023-06-18 17:51:40,577] [INFO] Task started: Blastn
[2023-06-18 17:51:40,577] [INFO] Running command: blastn -query GCA_018664885.1_ASM1866488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg82f108d2-9fc3-42ee-a731-338acbd90745/dqc_reference/reference_markers_gtdb.fasta -out GCA_018664885.1_ASM1866488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:41,454] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:41,460] [INFO] Selected 8 target genomes.
[2023-06-18 17:51:41,461] [INFO] Target genome list was writen to GCA_018664885.1_ASM1866488v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:51:41,486] [INFO] Task started: fastANI
[2023-06-18 17:51:41,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgae99fb7f-4d0b-4109-a300-c2fcf540a3be/GCA_018664885.1_ASM1866488v1_genomic.fna.gz --refList GCA_018664885.1_ASM1866488v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018664885.1_ASM1866488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:51:45,465] [INFO] Task succeeded: fastANI
[2023-06-18 17:51:45,472] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:51:45,473] [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_018650845.1	s__UBA1328 sp018650845	99.7001	641	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.74	99.74	0.93	0.93	2	conclusive
GCA_018649665.1	s__UBA1328 sp018649665	82.0701	345	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018673955.1	s__UBA1328 sp018673955	79.7238	293	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.55	99.47	0.91	0.89	13	-
GCA_012959765.1	s__UBA1328 sp012959765	78.7407	309	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.88	99.88	0.97	0.97	2	-
GCA_013204545.1	s__UBA1328 sp013204545	78.0884	244	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002501045.1	s__UBA1328 sp002501045	78.0451	232	687	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__UBA1151;f__UBA1328;g__UBA1328	95.0	99.73	99.73	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2023-06-18 17:51:45,476] [INFO] GTDB search result was written to GCA_018664885.1_ASM1866488v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:51:45,478] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:51:45,484] [INFO] DFAST_QC result json was written to GCA_018664885.1_ASM1866488v1_genomic.fna/dqc_result.json
[2023-06-18 17:51:45,484] [INFO] DFAST_QC completed!
[2023-06-18 17:51:45,484] [INFO] Total running time: 0h0m44s