[2023-06-14 01:47:37,325] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:47:37,327] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:47:37,328] [INFO] DQC Reference Directory: /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference
[2023-06-14 01:47:38,623] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:47:38,624] [INFO] Task started: Prodigal
[2023-06-14 01:47:38,624] [INFO] Running command: gunzip -c /var/lib/cwl/stg16953718-bab9-4dad-8065-c4ed118157e5/GCA_022508895.1_ASM2250889v1_genomic.fna.gz | prodigal -d GCA_022508895.1_ASM2250889v1_genomic.fna/cds.fna -a GCA_022508895.1_ASM2250889v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:47:44,097] [INFO] Task succeeded: Prodigal
[2023-06-14 01:47:44,098] [INFO] Task started: HMMsearch
[2023-06-14 01:47:44,098] [INFO] Running command: hmmsearch --tblout GCA_022508895.1_ASM2250889v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/reference_markers.hmm GCA_022508895.1_ASM2250889v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:47:44,373] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:47:44,374] [INFO] Found 6/6 markers.
[2023-06-14 01:47:44,436] [INFO] Query marker FASTA was written to GCA_022508895.1_ASM2250889v1_genomic.fna/markers.fasta
[2023-06-14 01:47:44,437] [INFO] Task started: Blastn
[2023-06-14 01:47:44,438] [INFO] Running command: blastn -query GCA_022508895.1_ASM2250889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/reference_markers.fasta -out GCA_022508895.1_ASM2250889v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:47:45,068] [INFO] Task succeeded: Blastn
[2023-06-14 01:47:45,077] [INFO] Selected 15 target genomes.
[2023-06-14 01:47:45,078] [INFO] Target genome list was writen to GCA_022508895.1_ASM2250889v1_genomic.fna/target_genomes.txt
[2023-06-14 01:47:45,082] [INFO] Task started: fastANI
[2023-06-14 01:47:45,083] [INFO] Running command: fastANI --query /var/lib/cwl/stg16953718-bab9-4dad-8065-c4ed118157e5/GCA_022508895.1_ASM2250889v1_genomic.fna.gz --refList GCA_022508895.1_ASM2250889v1_genomic.fna/target_genomes.txt --output GCA_022508895.1_ASM2250889v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:47:52,692] [INFO] Task succeeded: fastANI
[2023-06-14 01:47:52,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:47:52,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:47:52,694] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:47:52,695] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:47:52,695] [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
--------------------------------------------------------------------------------
[2023-06-14 01:47:52,696] [INFO] DFAST Taxonomy check result was written to GCA_022508895.1_ASM2250889v1_genomic.fna/tc_result.tsv
[2023-06-14 01:47:52,697] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:47:52,697] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:47:52,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/checkm_data
[2023-06-14 01:47:52,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:47:52,739] [INFO] Task started: CheckM
[2023-06-14 01:47:52,739] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022508895.1_ASM2250889v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022508895.1_ASM2250889v1_genomic.fna/checkm_input GCA_022508895.1_ASM2250889v1_genomic.fna/checkm_result
[2023-06-14 01:48:16,002] [INFO] Task succeeded: CheckM
[2023-06-14 01:48:16,004] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:48:16,028] [INFO] ===== Completeness check finished =====
[2023-06-14 01:48:16,028] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:48:16,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022508895.1_ASM2250889v1_genomic.fna/markers.fasta)
[2023-06-14 01:48:16,029] [INFO] Task started: Blastn
[2023-06-14 01:48:16,029] [INFO] Running command: blastn -query GCA_022508895.1_ASM2250889v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55512b53-ca05-4f60-b0f4-bd92294af170/dqc_reference/reference_markers_gtdb.fasta -out GCA_022508895.1_ASM2250889v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:48:17,093] [INFO] Task succeeded: Blastn
[2023-06-14 01:48:17,098] [INFO] Selected 25 target genomes.
[2023-06-14 01:48:17,098] [INFO] Target genome list was writen to GCA_022508895.1_ASM2250889v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:48:17,162] [INFO] Task started: fastANI
[2023-06-14 01:48:17,163] [INFO] Running command: fastANI --query /var/lib/cwl/stg16953718-bab9-4dad-8065-c4ed118157e5/GCA_022508895.1_ASM2250889v1_genomic.fna.gz --refList GCA_022508895.1_ASM2250889v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022508895.1_ASM2250889v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:48:27,804] [INFO] Task succeeded: fastANI
[2023-06-14 01:48:27,817] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-14 01:48:27,817] [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_014799365.1	s__Ruminiclostridium_E sp014799365	77.6392	148	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	97.60	97.60	0.81	0.81	2	-
GCA_014799325.1	s__Ruminiclostridium_E sp014799325	77.457	135	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588335.1	s__Ruminiclostridium_E sp910588335	77.2457	108	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910579265.1	s__Ruminiclostridium_E sp910579265	77.0341	76	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017635675.1	s__Ruminiclostridium_E sp017635675	76.8041	62	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003508605.1	s__Ruminiclostridium_E sp003508605	76.74	98	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585505.1	s__Ruminiclostridium_E sp910585505	76.7394	116	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017941355.1	s__Ruminiclostridium_E sp017941355	76.4548	65	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900542145.1	s__CAG-115 sp003507295	76.4075	54	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__CAG-115	95.0	98.16	97.02	0.91	0.87	5	-
GCA_900768675.1	s__Ruminiclostridium_E sp900768675	76.3517	64	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905235805.1	s__Ruminiclostridium_E sp905235805	76.1454	71	699	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminiclostridium_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-14 01:48:27,819] [INFO] GTDB search result was written to GCA_022508895.1_ASM2250889v1_genomic.fna/result_gtdb.tsv
[2023-06-14 01:48:27,820] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:48:27,823] [INFO] DFAST_QC result json was written to GCA_022508895.1_ASM2250889v1_genomic.fna/dqc_result.json
[2023-06-14 01:48:27,823] [INFO] DFAST_QC completed!
[2023-06-14 01:48:27,823] [INFO] Total running time: 0h0m50s