[2023-06-30 22:23:02,405] [INFO] DFAST_QC pipeline started.
[2023-06-30 22:23:02,408] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 22:23:02,408] [INFO] DQC Reference Directory: /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference
[2023-06-30 22:23:03,968] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 22:23:03,969] [INFO] Task started: Prodigal
[2023-06-30 22:23:03,969] [INFO] Running command: gunzip -c /var/lib/cwl/stge67ad116-1ef8-400d-b4a8-97845fa5621c/GCA_024696145.1_ASM2469614v1_genomic.fna.gz | prodigal -d GCA_024696145.1_ASM2469614v1_genomic.fna/cds.fna -a GCA_024696145.1_ASM2469614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 22:23:13,057] [INFO] Task succeeded: Prodigal
[2023-06-30 22:23:13,058] [INFO] Task started: HMMsearch
[2023-06-30 22:23:13,058] [INFO] Running command: hmmsearch --tblout GCA_024696145.1_ASM2469614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/reference_markers.hmm GCA_024696145.1_ASM2469614v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 22:23:13,272] [INFO] Task succeeded: HMMsearch
[2023-06-30 22:23:13,274] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge67ad116-1ef8-400d-b4a8-97845fa5621c/GCA_024696145.1_ASM2469614v1_genomic.fna.gz]
[2023-06-30 22:23:13,295] [INFO] Query marker FASTA was written to GCA_024696145.1_ASM2469614v1_genomic.fna/markers.fasta
[2023-06-30 22:23:13,295] [INFO] Task started: Blastn
[2023-06-30 22:23:13,295] [INFO] Running command: blastn -query GCA_024696145.1_ASM2469614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/reference_markers.fasta -out GCA_024696145.1_ASM2469614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:13,970] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:13,974] [INFO] Selected 25 target genomes.
[2023-06-30 22:23:13,974] [INFO] Target genome list was writen to GCA_024696145.1_ASM2469614v1_genomic.fna/target_genomes.txt
[2023-06-30 22:23:13,991] [INFO] Task started: fastANI
[2023-06-30 22:23:13,992] [INFO] Running command: fastANI --query /var/lib/cwl/stge67ad116-1ef8-400d-b4a8-97845fa5621c/GCA_024696145.1_ASM2469614v1_genomic.fna.gz --refList GCA_024696145.1_ASM2469614v1_genomic.fna/target_genomes.txt --output GCA_024696145.1_ASM2469614v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 22:23:27,432] [INFO] Task succeeded: fastANI
[2023-06-30 22:23:27,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 22:23:27,433] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 22:23:27,436] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 22:23:27,436] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 22:23:27,437] [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
--------------------------------------------------------------------------------
[2023-06-30 22:23:27,439] [INFO] DFAST Taxonomy check result was written to GCA_024696145.1_ASM2469614v1_genomic.fna/tc_result.tsv
[2023-06-30 22:23:27,440] [INFO] ===== Taxonomy check completed =====
[2023-06-30 22:23:27,441] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 22:23:27,441] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/checkm_data
[2023-06-30 22:23:27,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 22:23:27,476] [INFO] Task started: CheckM
[2023-06-30 22:23:27,476] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024696145.1_ASM2469614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024696145.1_ASM2469614v1_genomic.fna/checkm_input GCA_024696145.1_ASM2469614v1_genomic.fna/checkm_result
[2023-06-30 22:23:57,144] [INFO] Task succeeded: CheckM
[2023-06-30 22:23:57,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 22:23:57,166] [INFO] ===== Completeness check finished =====
[2023-06-30 22:23:57,166] [INFO] ===== Start GTDB Search =====
[2023-06-30 22:23:57,166] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024696145.1_ASM2469614v1_genomic.fna/markers.fasta)
[2023-06-30 22:23:57,167] [INFO] Task started: Blastn
[2023-06-30 22:23:57,167] [INFO] Running command: blastn -query GCA_024696145.1_ASM2469614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08629e56-b15c-4ccb-8589-58bf76a2e723/dqc_reference/reference_markers_gtdb.fasta -out GCA_024696145.1_ASM2469614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 22:23:58,302] [INFO] Task succeeded: Blastn
[2023-06-30 22:23:58,306] [INFO] Selected 24 target genomes.
[2023-06-30 22:23:58,306] [INFO] Target genome list was writen to GCA_024696145.1_ASM2469614v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 22:23:58,371] [INFO] Task started: fastANI
[2023-06-30 22:23:58,371] [INFO] Running command: fastANI --query /var/lib/cwl/stge67ad116-1ef8-400d-b4a8-97845fa5621c/GCA_024696145.1_ASM2469614v1_genomic.fna.gz --refList GCA_024696145.1_ASM2469614v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024696145.1_ASM2469614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 22:24:06,492] [INFO] Task succeeded: fastANI
[2023-06-30 22:24:06,512] [INFO] Found 22 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 22:24:06,512] [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_900320385.1	s__Cryptobacteroides sp900320385	97.6399	377	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	99.21	98.43	0.92	0.86	3	conclusive
GCA_017551405.1	s__Cryptobacteroides sp017551405	79.365	124	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905236955.1	s__Cryptobacteroides sp905236955	78.3914	116	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902762655.1	s__Cryptobacteroides sp902762655	78.2178	94	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.07	0.81	0.76	4	-
GCA_016283985.1	s__Cryptobacteroides sp016283985	78.0949	104	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017412645.1	s__Cryptobacteroides sp017412645	78.0714	141	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016287875.1	s__Cryptobacteroides sp016287875	78.0616	116	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469425.1	s__Cryptobacteroides sp017469425	77.9595	104	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317065.1	s__Cryptobacteroides sp900317065	77.9462	106	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.61	96.75	0.82	0.75	6	-
GCA_017617495.1	s__Cryptobacteroides sp017617495	77.9429	107	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016291185.1	s__Cryptobacteroides sp016291185	77.8028	88	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319975.1	s__Cryptobacteroides sp900319975	77.7596	97	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.34	97.18	0.88	0.88	3	-
GCA_902782225.1	s__Cryptobacteroides sp902782225	77.7519	106	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.55	97.13	0.87	0.83	3	-
GCA_900167895.1	s__Cryptobacteroides sp900167895	77.6304	119	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.18	97.90	0.94	0.93	3	-
GCA_017427385.1	s__Cryptobacteroides sp017427385	77.6161	115	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017535125.1	s__Cryptobacteroides sp017535125	77.4225	88	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017620335.1	s__Cryptobacteroides sp017620335	77.4112	100	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017554135.1	s__Cryptobacteroides sp017554135	77.2547	70	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453565.1	s__Cryptobacteroides sp017453565	77.2454	101	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780175.1	s__Cryptobacteroides sp902780175	77.1699	92	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	95.78	95.78	0.73	0.73	2	-
GCA_017614795.1	s__Cryptobacteroides sp017614795	77.0817	107	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017454905.1	s__Cryptobacteroides sp017454905	77.0115	102	470	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 22:24:06,514] [INFO] GTDB search result was written to GCA_024696145.1_ASM2469614v1_genomic.fna/result_gtdb.tsv
[2023-06-30 22:24:06,514] [INFO] ===== GTDB Search completed =====
[2023-06-30 22:24:06,518] [INFO] DFAST_QC result json was written to GCA_024696145.1_ASM2469614v1_genomic.fna/dqc_result.json
[2023-06-30 22:24:06,518] [INFO] DFAST_QC completed!
[2023-06-30 22:24:06,518] [INFO] Total running time: 0h1m4s