[2023-06-13 09:48:58,305] [INFO] DFAST_QC pipeline started.
[2023-06-13 09:48:58,308] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 09:48:58,308] [INFO] DQC Reference Directory: /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference
[2023-06-13 09:48:59,555] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 09:48:59,556] [INFO] Task started: Prodigal
[2023-06-13 09:48:59,556] [INFO] Running command: gunzip -c /var/lib/cwl/stg616f335a-bc5b-4785-b76f-cc9947b70879/GCA_022708655.1_ASM2270865v1_genomic.fna.gz | prodigal -d GCA_022708655.1_ASM2270865v1_genomic.fna/cds.fna -a GCA_022708655.1_ASM2270865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 09:49:12,264] [INFO] Task succeeded: Prodigal
[2023-06-13 09:49:12,264] [INFO] Task started: HMMsearch
[2023-06-13 09:49:12,265] [INFO] Running command: hmmsearch --tblout GCA_022708655.1_ASM2270865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/reference_markers.hmm GCA_022708655.1_ASM2270865v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 09:49:12,539] [INFO] Task succeeded: HMMsearch
[2023-06-13 09:49:12,542] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg616f335a-bc5b-4785-b76f-cc9947b70879/GCA_022708655.1_ASM2270865v1_genomic.fna.gz]
[2023-06-13 09:49:12,576] [INFO] Query marker FASTA was written to GCA_022708655.1_ASM2270865v1_genomic.fna/markers.fasta
[2023-06-13 09:49:12,576] [INFO] Task started: Blastn
[2023-06-13 09:49:12,576] [INFO] Running command: blastn -query GCA_022708655.1_ASM2270865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/reference_markers.fasta -out GCA_022708655.1_ASM2270865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:49:13,127] [INFO] Task succeeded: Blastn
[2023-06-13 09:49:13,132] [INFO] Selected 25 target genomes.
[2023-06-13 09:49:13,133] [INFO] Target genome list was writen to GCA_022708655.1_ASM2270865v1_genomic.fna/target_genomes.txt
[2023-06-13 09:49:13,138] [INFO] Task started: fastANI
[2023-06-13 09:49:13,139] [INFO] Running command: fastANI --query /var/lib/cwl/stg616f335a-bc5b-4785-b76f-cc9947b70879/GCA_022708655.1_ASM2270865v1_genomic.fna.gz --refList GCA_022708655.1_ASM2270865v1_genomic.fna/target_genomes.txt --output GCA_022708655.1_ASM2270865v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 09:49:27,825] [INFO] Task succeeded: fastANI
[2023-06-13 09:49:27,826] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 09:49:27,826] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 09:49:27,828] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 09:49:27,828] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 09:49:27,828] [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
--------------------------------------------------------------------------------
[2023-06-13 09:49:27,831] [INFO] DFAST Taxonomy check result was written to GCA_022708655.1_ASM2270865v1_genomic.fna/tc_result.tsv
[2023-06-13 09:49:27,832] [INFO] ===== Taxonomy check completed =====
[2023-06-13 09:49:27,832] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 09:49:27,832] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/checkm_data
[2023-06-13 09:49:27,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 09:49:27,869] [INFO] Task started: CheckM
[2023-06-13 09:49:27,870] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022708655.1_ASM2270865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022708655.1_ASM2270865v1_genomic.fna/checkm_input GCA_022708655.1_ASM2270865v1_genomic.fna/checkm_result
[2023-06-13 09:50:08,487] [INFO] Task succeeded: CheckM
[2023-06-13 09:50:08,490] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.77%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 09:50:08,511] [INFO] ===== Completeness check finished =====
[2023-06-13 09:50:08,512] [INFO] ===== Start GTDB Search =====
[2023-06-13 09:50:08,512] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022708655.1_ASM2270865v1_genomic.fna/markers.fasta)
[2023-06-13 09:50:08,512] [INFO] Task started: Blastn
[2023-06-13 09:50:08,512] [INFO] Running command: blastn -query GCA_022708655.1_ASM2270865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60722b2d-d56c-4c90-8c9f-5525955a44dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_022708655.1_ASM2270865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 09:50:09,237] [INFO] Task succeeded: Blastn
[2023-06-13 09:50:09,242] [INFO] Selected 16 target genomes.
[2023-06-13 09:50:09,243] [INFO] Target genome list was writen to GCA_022708655.1_ASM2270865v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 09:50:09,252] [INFO] Task started: fastANI
[2023-06-13 09:50:09,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg616f335a-bc5b-4785-b76f-cc9947b70879/GCA_022708655.1_ASM2270865v1_genomic.fna.gz --refList GCA_022708655.1_ASM2270865v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022708655.1_ASM2270865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 09:50:15,250] [INFO] Task succeeded: fastANI
[2023-06-13 09:50:15,277] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 09:50:15,277] [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_002340405.1	s__UBA1179 sp002340405	98.2333	356	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.50	98.24	0.87	0.80	7	conclusive
GCA_900318995.1	s__UBA1179 sp900318995	77.6151	115	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.89	96.18	0.89	0.85	8	-
GCA_905234745.1	s__UBA1179 sp905234745	77.3277	111	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235565.1	s__UBA1179 sp905235565	77.2673	121	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319225.1	s__UBA1179 sp900319225	77.2238	113	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	98.54	97.96	0.93	0.90	5	-
GCA_902763885.1	s__UBA1179 sp902763885	77.2003	109	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760965.1	s__UBA1179 sp902760965	77.1369	110	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.44	97.44	0.87	0.87	2	-
GCA_017633615.1	s__UBA1179 sp017633615	77.1137	109	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551845.1	s__UBA1179 sp017551845	77.0721	123	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902799685.1	s__UBA1179 sp902799685	77.0274	114	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	96.39	96.39	0.82	0.82	2	-
GCA_002310015.1	s__UBA1179 sp002310015	77.0078	91	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017612875.1	s__UBA1179 sp017612875	76.9691	97	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551925.1	s__UBA1179 sp017551925	76.9637	113	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774275.1	s__UBA1179 sp902774275	76.8221	101	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017651315.1	s__UBA1179 sp017651315	76.7597	124	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	97.72	97.72	0.81	0.81	2	-
GCA_002310175.1	s__UBA1179 sp002310175	76.6573	103	665	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__UBA1179	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 09:50:15,280] [INFO] GTDB search result was written to GCA_022708655.1_ASM2270865v1_genomic.fna/result_gtdb.tsv
[2023-06-13 09:50:15,281] [INFO] ===== GTDB Search completed =====
[2023-06-13 09:50:15,283] [INFO] DFAST_QC result json was written to GCA_022708655.1_ASM2270865v1_genomic.fna/dqc_result.json
[2023-06-13 09:50:15,284] [INFO] DFAST_QC completed!
[2023-06-13 09:50:15,284] [INFO] Total running time: 0h1m17s