[2023-06-08 20:30:14,372] [INFO] DFAST_QC pipeline started.
[2023-06-08 20:30:14,375] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 20:30:14,375] [INFO] DQC Reference Directory: /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference
[2023-06-08 20:30:16,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 20:30:16,972] [INFO] Task started: Prodigal
[2023-06-08 20:30:16,973] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4181835-8de5-437e-ad3e-cb085f3d8cd9/GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cds.fna -a GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 20:30:19,263] [INFO] Task succeeded: Prodigal
[2023-06-08 20:30:19,264] [INFO] Task started: HMMsearch
[2023-06-08 20:30:19,264] [INFO] Running command: hmmsearch --tblout GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/reference_markers.hmm GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-08 20:30:19,469] [INFO] Task succeeded: HMMsearch
[2023-06-08 20:30:19,470] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb4181835-8de5-437e-ad3e-cb085f3d8cd9/GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz]
[2023-06-08 20:30:19,484] [INFO] Query marker FASTA was written to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-08 20:30:19,484] [INFO] Task started: Blastn
[2023-06-08 20:30:19,484] [INFO] Running command: blastn -query GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/reference_markers.fasta -out GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:30:21,070] [INFO] Task succeeded: Blastn
[2023-06-08 20:30:21,075] [INFO] Selected 22 target genomes.
[2023-06-08 20:30:21,076] [INFO] Target genome list was writen to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-08 20:30:21,079] [INFO] Task started: fastANI
[2023-06-08 20:30:21,079] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4181835-8de5-437e-ad3e-cb085f3d8cd9/GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 20:30:30,976] [INFO] Task succeeded: fastANI
[2023-06-08 20:30:30,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 20:30:30,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 20:30:30,983] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 20:30:30,983] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 20:30:30,984] [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
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	77.1154	50	236	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 20:30:30,986] [INFO] DFAST Taxonomy check result was written to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-08 20:30:30,986] [INFO] ===== Taxonomy check completed =====
[2023-06-08 20:30:30,987] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 20:30:30,987] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/checkm_data
[2023-06-08 20:30:30,988] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 20:30:31,000] [INFO] Task started: CheckM
[2023-06-08 20:30:31,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_input GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/checkm_result
[2023-06-08 20:30:45,583] [INFO] Task succeeded: CheckM
[2023-06-08 20:30:45,584] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.64%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 20:30:45,598] [INFO] ===== Completeness check finished =====
[2023-06-08 20:30:45,598] [INFO] ===== Start GTDB Search =====
[2023-06-08 20:30:45,599] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-08 20:30:45,599] [INFO] Task started: Blastn
[2023-06-08 20:30:45,599] [INFO] Running command: blastn -query GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgaeabdb0d-ca1e-42ba-b9b8-7fe88a43413b/dqc_reference/reference_markers_gtdb.fasta -out GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 20:30:46,692] [INFO] Task succeeded: Blastn
[2023-06-08 20:30:46,696] [INFO] Selected 15 target genomes.
[2023-06-08 20:30:46,696] [INFO] Target genome list was writen to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 20:30:46,697] [INFO] Task started: fastANI
[2023-06-08 20:30:46,697] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4181835-8de5-437e-ad3e-cb085f3d8cd9/GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna.gz --refList GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 20:30:51,178] [INFO] Task succeeded: fastANI
[2023-06-08 20:30:51,200] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 20:30:51,201] [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_016295615.1	s__ER4 sp016295615	99.096	205	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.52	97.90	0.85	0.84	3	conclusive
GCF_018918025.1	s__ER4 sp900317525	80.1873	168	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.58	97.23	0.91	0.84	22	-
GCA_002405995.1	s__ER4 sp002405995	80.0806	156	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	99.39	99.39	0.82	0.82	2	-
GCA_900546295.1	s__ER4 sp900546295	80.0553	152	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	98.01	98.01	0.87	0.87	2	-
GCA_900763705.1	s__ER4 sp900763705	79.8108	126	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900550165.1	s__ER4 sp900550165	79.7876	148	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.79	96.53	0.85	0.84	4	-
GCA_900556145.1	s__ER4 sp900556145	79.7495	98	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900768135.1	s__ER4 sp900768135	79.7365	151	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003522105.1	s__ER4 sp003522105	79.6325	149	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	97.35	97.09	0.78	0.74	7	-
GCF_000765235.1	s__ER4 sp000765235	79.6225	151	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	96.82	96.40	0.83	0.70	19	-
GCA_900552015.1	s__ER4 sp900552015	79.5477	139	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	100.00	100.00	0.99	0.99	2	-
GCA_015067435.1	s__ER4 sp015067435	79.3001	136	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902779695.1	s__ER4 sp902779695	78.9128	106	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068465.1	s__ER4 sp015068465	78.836	123	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458025.1	s__ER4 sp017458025	78.643	101	236	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__ER4	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 20:30:51,203] [INFO] GTDB search result was written to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-08 20:30:51,204] [INFO] ===== GTDB Search completed =====
[2023-06-08 20:30:51,208] [INFO] DFAST_QC result json was written to GCA_945971215.1_SRR15725434_bin.9_metaWRAP_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-08 20:30:51,209] [INFO] DFAST_QC completed!
[2023-06-08 20:30:51,209] [INFO] Total running time: 0h0m37s