[2023-06-05 15:04:30,129] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:04:30,132] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:04:30,132] [INFO] DQC Reference Directory: /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference
[2023-06-05 15:04:31,354] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:04:31,355] [INFO] Task started: Prodigal
[2023-06-05 15:04:31,355] [INFO] Running command: gunzip -c /var/lib/cwl/stg6d13e5a0-73ae-4b75-b29e-cda2c92ef965/GCA_004556005.1_ASM455600v1_genomic.fna.gz | prodigal -d GCA_004556005.1_ASM455600v1_genomic.fna/cds.fna -a GCA_004556005.1_ASM455600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:04:41,265] [INFO] Task succeeded: Prodigal
[2023-06-05 15:04:41,265] [INFO] Task started: HMMsearch
[2023-06-05 15:04:41,266] [INFO] Running command: hmmsearch --tblout GCA_004556005.1_ASM455600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/reference_markers.hmm GCA_004556005.1_ASM455600v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:04:41,536] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:04:41,538] [INFO] Found 6/6 markers.
[2023-06-05 15:04:41,563] [INFO] Query marker FASTA was written to GCA_004556005.1_ASM455600v1_genomic.fna/markers.fasta
[2023-06-05 15:04:41,564] [INFO] Task started: Blastn
[2023-06-05 15:04:41,564] [INFO] Running command: blastn -query GCA_004556005.1_ASM455600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/reference_markers.fasta -out GCA_004556005.1_ASM455600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:04:42,140] [INFO] Task succeeded: Blastn
[2023-06-05 15:04:42,145] [INFO] Selected 31 target genomes.
[2023-06-05 15:04:42,146] [INFO] Target genome list was writen to GCA_004556005.1_ASM455600v1_genomic.fna/target_genomes.txt
[2023-06-05 15:04:42,186] [INFO] Task started: fastANI
[2023-06-05 15:04:42,186] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d13e5a0-73ae-4b75-b29e-cda2c92ef965/GCA_004556005.1_ASM455600v1_genomic.fna.gz --refList GCA_004556005.1_ASM455600v1_genomic.fna/target_genomes.txt --output GCA_004556005.1_ASM455600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:01,380] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:01,381] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:01,381] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:01,383] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:01,384] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 15:05:01,384] [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
--------------------------------------------------------------------------------
[2023-06-05 15:05:01,405] [INFO] DFAST Taxonomy check result was written to GCA_004556005.1_ASM455600v1_genomic.fna/tc_result.tsv
[2023-06-05 15:05:01,406] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:01,406] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:01,406] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/checkm_data
[2023-06-05 15:05:01,410] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:01,434] [INFO] Task started: CheckM
[2023-06-05 15:05:01,434] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004556005.1_ASM455600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004556005.1_ASM455600v1_genomic.fna/checkm_input GCA_004556005.1_ASM455600v1_genomic.fna/checkm_result
[2023-06-05 15:05:35,373] [INFO] Task succeeded: CheckM
[2023-06-05 15:05:35,374] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:05:35,394] [INFO] ===== Completeness check finished =====
[2023-06-05 15:05:35,394] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:05:35,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004556005.1_ASM455600v1_genomic.fna/markers.fasta)
[2023-06-05 15:05:35,395] [INFO] Task started: Blastn
[2023-06-05 15:05:35,396] [INFO] Running command: blastn -query GCA_004556005.1_ASM455600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11ab3070-0e39-41b0-823e-1c8d316606ea/dqc_reference/reference_markers_gtdb.fasta -out GCA_004556005.1_ASM455600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:36,234] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:36,239] [INFO] Selected 25 target genomes.
[2023-06-05 15:05:36,239] [INFO] Target genome list was writen to GCA_004556005.1_ASM455600v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:05:36,288] [INFO] Task started: fastANI
[2023-06-05 15:05:36,289] [INFO] Running command: fastANI --query /var/lib/cwl/stg6d13e5a0-73ae-4b75-b29e-cda2c92ef965/GCA_004556005.1_ASM455600v1_genomic.fna.gz --refList GCA_004556005.1_ASM455600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004556005.1_ASM455600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:05:45,112] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:45,125] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 15:05:45,125] [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_004556005.1	s__Cryptobacteroides sp004556005	100.0	587	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.66	98.30	0.85	0.82	5	conclusive
GCA_902787295.1	s__Cryptobacteroides sp902787295	78.4121	113	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.75	97.75	0.73	0.73	2	-
GCA_018064625.1	s__Cryptobacteroides sp018064625	78.2355	60	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900769905.1	s__Cryptobacteroides sp900769905	77.8882	113	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.32	98.32	0.78	0.78	2	-
GCA_018384035.1	s__Cryptobacteroides sp018384035	77.697	53	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900541925.1	s__Cryptobacteroides sp900541925	77.6892	90	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.89	97.86	0.90	0.88	3	-
GCA_900318565.1	s__Cryptobacteroides sp900318565	77.4708	79	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.62	96.86	0.83	0.73	9	-
GCA_902785785.1	s__Cryptobacteroides sp900321245	77.4545	63	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.82	95.44	0.88	0.77	10	-
GCA_001915575.1	s__Cryptobacteroides pullicola	77.4289	70	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.50	97.05	0.96	0.92	3	-
GCA_016295245.1	s__Cryptobacteroides sp016295245	77.3688	87	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	98.61	98.61	0.79	0.79	2	-
GCA_017458145.1	s__Cryptobacteroides sp017458145	77.1826	67	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017455065.1	s__Cryptobacteroides sp017455065	77.1362	76	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017616595.1	s__Cryptobacteroides sp017616595	77.1027	53	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551425.1	s__Cryptobacteroides sp017551425	77.0604	52	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902790635.1	s__Cryptobacteroides sp902790635	77.0417	69	590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 15:05:45,127] [INFO] GTDB search result was written to GCA_004556005.1_ASM455600v1_genomic.fna/result_gtdb.tsv
[2023-06-05 15:05:45,128] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:05:45,131] [INFO] DFAST_QC result json was written to GCA_004556005.1_ASM455600v1_genomic.fna/dqc_result.json
[2023-06-05 15:05:45,132] [INFO] DFAST_QC completed!
[2023-06-05 15:05:45,132] [INFO] Total running time: 0h1m15s