[2023-06-08 04:30:09,571] [INFO] DFAST_QC pipeline started.
[2023-06-08 04:30:09,573] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 04:30:09,573] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference
[2023-06-08 04:30:10,879] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 04:30:10,880] [INFO] Task started: Prodigal
[2023-06-08 04:30:10,881] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b81f8cd-3c4e-4ae0-ba03-a3d7efbcd380/GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 04:30:14,559] [INFO] Task succeeded: Prodigal
[2023-06-08 04:30:14,560] [INFO] Task started: HMMsearch
[2023-06-08 04:30:14,560] [INFO] Running command: hmmsearch --tblout GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/reference_markers.hmm GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 04:30:14,771] [INFO] Task succeeded: HMMsearch
[2023-06-08 04:30:14,772] [INFO] Found 6/6 markers.
[2023-06-08 04:30:14,788] [INFO] Query marker FASTA was written to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 04:30:14,788] [INFO] Task started: Blastn
[2023-06-08 04:30:14,789] [INFO] Running command: blastn -query GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/reference_markers.fasta -out GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:15,419] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:15,430] [INFO] Selected 20 target genomes.
[2023-06-08 04:30:15,430] [INFO] Target genome list was writen to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 04:30:15,452] [INFO] Task started: fastANI
[2023-06-08 04:30:15,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b81f8cd-3c4e-4ae0-ba03-a3d7efbcd380/GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 04:30:27,896] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:27,896] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 04:30:27,897] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 04:30:27,898] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 04:30:27,899] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 04:30:27,899] [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
--------------------------------------------------------------------------------
[2023-06-08 04:30:27,901] [INFO] DFAST Taxonomy check result was written to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 04:30:27,902] [INFO] ===== Taxonomy check completed =====
[2023-06-08 04:30:27,902] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 04:30:27,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/checkm_data
[2023-06-08 04:30:27,905] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 04:30:27,927] [INFO] Task started: CheckM
[2023-06-08 04:30:27,927] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 04:30:46,730] [INFO] Task succeeded: CheckM
[2023-06-08 04:30:46,731] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.28%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 04:30:46,750] [INFO] ===== Completeness check finished =====
[2023-06-08 04:30:46,750] [INFO] ===== Start GTDB Search =====
[2023-06-08 04:30:46,751] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 04:30:46,751] [INFO] Task started: Blastn
[2023-06-08 04:30:46,751] [INFO] Running command: blastn -query GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7e690cc-c328-4d7b-85b1-f03d565c7e9b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 04:30:47,651] [INFO] Task succeeded: Blastn
[2023-06-08 04:30:47,655] [INFO] Selected 11 target genomes.
[2023-06-08 04:30:47,656] [INFO] Target genome list was writen to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 04:30:47,658] [INFO] Task started: fastANI
[2023-06-08 04:30:47,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b81f8cd-3c4e-4ae0-ba03-a3d7efbcd380/GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 04:30:51,841] [INFO] Task succeeded: fastANI
[2023-06-08 04:30:51,855] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 04:30:51,856] [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_000431075.1	s__F23-B02 sp000431075	97.2767	382	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.66	0.87	0.84	6	conclusive
GCA_003533405.1	s__F23-B02 sp003533405	93.1572	340	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	96.88	96.88	0.79	0.79	2	-
GCA_016292445.1	s__F23-B02 sp016292445	83.0896	284	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	97.48	96.04	0.83	0.83	3	-
GCA_001916715.1	s__F23-B02 sp001916715	79.917	212	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.22	97.52	0.91	0.88	7	-
GCA_002472405.1	s__F23-B02 sp002472405	79.7339	216	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.11	97.78	0.86	0.83	6	-
GCA_002314685.1	s__F23-B02 sp002314685	79.7305	163	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004557075.1	s__F23-B02 sp004557075	79.5949	188	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	98.03	98.03	0.72	0.72	2	-
GCA_900772725.1	s__F23-B02 sp900772725	79.2838	132	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__F23-B02	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000432375.1	s__CAG-103 sp000432375	77.743	86	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_902786615.1	s__Limivicinus sp902786615	77.3891	68	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017411225.1	s__CAG-103 sp017411225	77.1555	50	405	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 04:30:51,858] [INFO] GTDB search result was written to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 04:30:51,859] [INFO] ===== GTDB Search completed =====
[2023-06-08 04:30:51,863] [INFO] DFAST_QC result json was written to GCA_945971715.1_SRR15725431_bin.41_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 04:30:51,863] [INFO] DFAST_QC completed!
[2023-06-08 04:30:51,863] [INFO] Total running time: 0h0m42s