[2023-06-28 13:08:18,233] [INFO] DFAST_QC pipeline started.
[2023-06-28 13:08:18,237] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 13:08:18,237] [INFO] DQC Reference Directory: /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference
[2023-06-28 13:08:19,650] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 13:08:19,656] [INFO] Task started: Prodigal
[2023-06-28 13:08:19,656] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3426925-d7fc-4140-8946-b1f27328ce2a/GCA_017476965.1_ASM1747696v1_genomic.fna.gz | prodigal -d GCA_017476965.1_ASM1747696v1_genomic.fna/cds.fna -a GCA_017476965.1_ASM1747696v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 13:08:24,294] [INFO] Task succeeded: Prodigal
[2023-06-28 13:08:24,295] [INFO] Task started: HMMsearch
[2023-06-28 13:08:24,295] [INFO] Running command: hmmsearch --tblout GCA_017476965.1_ASM1747696v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/reference_markers.hmm GCA_017476965.1_ASM1747696v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 13:08:24,574] [INFO] Task succeeded: HMMsearch
[2023-06-28 13:08:24,576] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd3426925-d7fc-4140-8946-b1f27328ce2a/GCA_017476965.1_ASM1747696v1_genomic.fna.gz]
[2023-06-28 13:08:24,604] [INFO] Query marker FASTA was written to GCA_017476965.1_ASM1747696v1_genomic.fna/markers.fasta
[2023-06-28 13:08:24,605] [INFO] Task started: Blastn
[2023-06-28 13:08:24,605] [INFO] Running command: blastn -query GCA_017476965.1_ASM1747696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/reference_markers.fasta -out GCA_017476965.1_ASM1747696v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:08:25,255] [INFO] Task succeeded: Blastn
[2023-06-28 13:08:25,261] [INFO] Selected 20 target genomes.
[2023-06-28 13:08:25,261] [INFO] Target genome list was writen to GCA_017476965.1_ASM1747696v1_genomic.fna/target_genomes.txt
[2023-06-28 13:08:25,282] [INFO] Task started: fastANI
[2023-06-28 13:08:25,283] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3426925-d7fc-4140-8946-b1f27328ce2a/GCA_017476965.1_ASM1747696v1_genomic.fna.gz --refList GCA_017476965.1_ASM1747696v1_genomic.fna/target_genomes.txt --output GCA_017476965.1_ASM1747696v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 13:08:44,979] [INFO] Task succeeded: fastANI
[2023-06-28 13:08:44,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 13:08:44,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 13:08:44,989] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 13:08:44,990] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 13:08:44,990] [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=ATCC 25963	GCA_900112715.1	54	54	type	True	74.8522	63	421	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.8402	66	421	95	below_threshold
Solirubrobacter pauli	strain=DSM 14954	GCA_003633755.1	166793	166793	type	True	74.8273	55	421	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 13:08:44,992] [INFO] DFAST Taxonomy check result was written to GCA_017476965.1_ASM1747696v1_genomic.fna/tc_result.tsv
[2023-06-28 13:08:44,993] [INFO] ===== Taxonomy check completed =====
[2023-06-28 13:08:44,993] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 13:08:44,993] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/checkm_data
[2023-06-28 13:08:44,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 13:08:45,022] [INFO] Task started: CheckM
[2023-06-28 13:08:45,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017476965.1_ASM1747696v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017476965.1_ASM1747696v1_genomic.fna/checkm_input GCA_017476965.1_ASM1747696v1_genomic.fna/checkm_result
[2023-06-28 13:09:04,660] [INFO] Task succeeded: CheckM
[2023-06-28 13:09:04,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-28 13:09:04,689] [INFO] ===== Completeness check finished =====
[2023-06-28 13:09:04,690] [INFO] ===== Start GTDB Search =====
[2023-06-28 13:09:04,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017476965.1_ASM1747696v1_genomic.fna/markers.fasta)
[2023-06-28 13:09:04,690] [INFO] Task started: Blastn
[2023-06-28 13:09:04,691] [INFO] Running command: blastn -query GCA_017476965.1_ASM1747696v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4f673251-9f4f-4d93-b143-50d5036d5676/dqc_reference/reference_markers_gtdb.fasta -out GCA_017476965.1_ASM1747696v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 13:09:05,596] [INFO] Task succeeded: Blastn
[2023-06-28 13:09:05,600] [INFO] Selected 8 target genomes.
[2023-06-28 13:09:05,600] [INFO] Target genome list was writen to GCA_017476965.1_ASM1747696v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 13:09:05,606] [INFO] Task started: fastANI
[2023-06-28 13:09:05,606] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3426925-d7fc-4140-8946-b1f27328ce2a/GCA_017476965.1_ASM1747696v1_genomic.fna.gz --refList GCA_017476965.1_ASM1747696v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017476965.1_ASM1747696v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 13:09:09,517] [INFO] Task succeeded: fastANI
[2023-06-28 13:09:09,531] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 13:09:09,531] [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_017476965.1	s__UBA3636 sp017476965	100.0	410	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	95.60	95.60	0.67	0.67	2	conclusive
GCA_902793555.1	s__UBA3636 sp902793555	80.4033	169	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902761575.1	s__UBA3636 sp902761575	80.3489	188	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	96.69	96.69	0.81	0.81	2	-
GCA_017413145.1	s__UBA3636 sp017413145	80.2276	154	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017457625.1	s__UBA3636 sp017457625	79.9625	163	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002448475.1	s__UBA3636 sp002448475	79.8152	199	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	97.08	96.88	0.80	0.71	3	-
GCA_017450425.1	s__UBA3636 sp017450425	78.1315	85	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__UBA3636	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012514445.1	s__JAAZAI01 sp012514445	77.2142	65	421	d__Bacteria;p__Verrucomicrobiota;c__Kiritimatiellae;o__RFP12;f__UBA3636;g__JAAZAI01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 13:09:09,534] [INFO] GTDB search result was written to GCA_017476965.1_ASM1747696v1_genomic.fna/result_gtdb.tsv
[2023-06-28 13:09:09,534] [INFO] ===== GTDB Search completed =====
[2023-06-28 13:09:09,537] [INFO] DFAST_QC result json was written to GCA_017476965.1_ASM1747696v1_genomic.fna/dqc_result.json
[2023-06-28 13:09:09,538] [INFO] DFAST_QC completed!
[2023-06-28 13:09:09,538] [INFO] Total running time: 0h0m51s