[2023-06-19 14:06:22,584] [INFO] DFAST_QC pipeline started.
[2023-06-19 14:06:22,588] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 14:06:22,588] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference
[2023-06-19 14:06:23,767] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 14:06:23,768] [INFO] Task started: Prodigal
[2023-06-19 14:06:23,769] [INFO] Running command: gunzip -c /var/lib/cwl/stg3059f655-c0f4-46b6-bb8e-061ae0349a19/GCA_018674875.1_ASM1867487v1_genomic.fna.gz | prodigal -d GCA_018674875.1_ASM1867487v1_genomic.fna/cds.fna -a GCA_018674875.1_ASM1867487v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 14:06:38,687] [INFO] Task succeeded: Prodigal
[2023-06-19 14:06:38,687] [INFO] Task started: HMMsearch
[2023-06-19 14:06:38,688] [INFO] Running command: hmmsearch --tblout GCA_018674875.1_ASM1867487v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/reference_markers.hmm GCA_018674875.1_ASM1867487v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 14:06:38,952] [INFO] Task succeeded: HMMsearch
[2023-06-19 14:06:38,954] [INFO] Found 6/6 markers.
[2023-06-19 14:06:39,021] [INFO] Query marker FASTA was written to GCA_018674875.1_ASM1867487v1_genomic.fna/markers.fasta
[2023-06-19 14:06:39,021] [INFO] Task started: Blastn
[2023-06-19 14:06:39,021] [INFO] Running command: blastn -query GCA_018674875.1_ASM1867487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/reference_markers.fasta -out GCA_018674875.1_ASM1867487v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:06:39,597] [INFO] Task succeeded: Blastn
[2023-06-19 14:06:39,601] [INFO] Selected 38 target genomes.
[2023-06-19 14:06:39,601] [INFO] Target genome list was writen to GCA_018674875.1_ASM1867487v1_genomic.fna/target_genomes.txt
[2023-06-19 14:06:39,604] [INFO] Task started: fastANI
[2023-06-19 14:06:39,604] [INFO] Running command: fastANI --query /var/lib/cwl/stg3059f655-c0f4-46b6-bb8e-061ae0349a19/GCA_018674875.1_ASM1867487v1_genomic.fna.gz --refList GCA_018674875.1_ASM1867487v1_genomic.fna/target_genomes.txt --output GCA_018674875.1_ASM1867487v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 14:07:08,295] [INFO] Task succeeded: fastANI
[2023-06-19 14:07:08,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 14:07:08,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 14:07:08,300] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 14:07:08,300] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 14:07:08,300] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.7141	54	1743	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.6526	52	1743	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 14:07:08,303] [INFO] DFAST Taxonomy check result was written to GCA_018674875.1_ASM1867487v1_genomic.fna/tc_result.tsv
[2023-06-19 14:07:08,303] [INFO] ===== Taxonomy check completed =====
[2023-06-19 14:07:08,303] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 14:07:08,303] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/checkm_data
[2023-06-19 14:07:08,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 14:07:08,363] [INFO] Task started: CheckM
[2023-06-19 14:07:08,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018674875.1_ASM1867487v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018674875.1_ASM1867487v1_genomic.fna/checkm_input GCA_018674875.1_ASM1867487v1_genomic.fna/checkm_result
[2023-06-19 14:07:52,322] [INFO] Task succeeded: CheckM
[2023-06-19 14:07:52,323] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.93%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 14:07:52,347] [INFO] ===== Completeness check finished =====
[2023-06-19 14:07:52,347] [INFO] ===== Start GTDB Search =====
[2023-06-19 14:07:52,347] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018674875.1_ASM1867487v1_genomic.fna/markers.fasta)
[2023-06-19 14:07:52,347] [INFO] Task started: Blastn
[2023-06-19 14:07:52,348] [INFO] Running command: blastn -query GCA_018674875.1_ASM1867487v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f94622a-ebf2-4ebc-a86a-993c3acfaf26/dqc_reference/reference_markers_gtdb.fasta -out GCA_018674875.1_ASM1867487v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 14:07:53,124] [INFO] Task succeeded: Blastn
[2023-06-19 14:07:53,129] [INFO] Selected 23 target genomes.
[2023-06-19 14:07:53,129] [INFO] Target genome list was writen to GCA_018674875.1_ASM1867487v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 14:07:53,155] [INFO] Task started: fastANI
[2023-06-19 14:07:53,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg3059f655-c0f4-46b6-bb8e-061ae0349a19/GCA_018674875.1_ASM1867487v1_genomic.fna.gz --refList GCA_018674875.1_ASM1867487v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018674875.1_ASM1867487v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 14:08:13,543] [INFO] Task succeeded: fastANI
[2023-06-19 14:08:13,551] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 14:08:13,552] [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_018672475.1	s__GCA-2724215 sp018672475	99.7797	1677	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.78	99.75	0.95	0.94	9	conclusive
GCA_015660315.1	s__GCA-2724215 sp015660315	93.0667	1116	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002724215.1	s__GCA-2724215 sp002724215	77.9416	643	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009841115.1	s__GCA-2724215 sp009841115	76.897	311	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.89	99.89	0.98	0.96	3	-
GCA_009840005.1	s__GCA-2724215 sp009840005	76.74	315	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	99.94	99.94	0.99	0.99	2	-
GCA_009845645.1	s__GCA-2724215 sp009845645	76.5088	181	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007571365.1	s__GCA-2724215 sp007571365	76.4662	238	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__GCA-2724215	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726335.1	s__UBA8231 sp002726335	75.5041	52	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__UBA8231	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016867395.1	s__SICG01 sp016867395	75.4948	76	1743	d__Bacteria;p__Latescibacterota;c__UBA2968;o__UBA8231;f__UBA8231;g__SICG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 14:08:13,554] [INFO] GTDB search result was written to GCA_018674875.1_ASM1867487v1_genomic.fna/result_gtdb.tsv
[2023-06-19 14:08:13,554] [INFO] ===== GTDB Search completed =====
[2023-06-19 14:08:13,557] [INFO] DFAST_QC result json was written to GCA_018674875.1_ASM1867487v1_genomic.fna/dqc_result.json
[2023-06-19 14:08:13,557] [INFO] DFAST_QC completed!
[2023-06-19 14:08:13,557] [INFO] Total running time: 0h1m51s