[2023-06-13 05:50:02,260] [INFO] DFAST_QC pipeline started.
[2023-06-13 05:50:02,263] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 05:50:02,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference
[2023-06-13 05:50:03,594] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 05:50:03,597] [INFO] Task started: Prodigal
[2023-06-13 05:50:03,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b59edaf-3067-4ab4-8c8f-cdabf9a648e1/GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 05:50:11,013] [INFO] Task succeeded: Prodigal
[2023-06-13 05:50:11,014] [INFO] Task started: HMMsearch
[2023-06-13 05:50:11,014] [INFO] Running command: hmmsearch --tblout GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/reference_markers.hmm GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 05:50:11,260] [INFO] Task succeeded: HMMsearch
[2023-06-13 05:50:11,262] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0b59edaf-3067-4ab4-8c8f-cdabf9a648e1/GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-13 05:50:11,293] [INFO] Query marker FASTA was written to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-13 05:50:11,293] [INFO] Task started: Blastn
[2023-06-13 05:50:11,293] [INFO] Running command: blastn -query GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/reference_markers.fasta -out GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:11,880] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:11,884] [INFO] Selected 24 target genomes.
[2023-06-13 05:50:11,885] [INFO] Target genome list was writen to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-13 05:50:11,887] [INFO] Task started: fastANI
[2023-06-13 05:50:11,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b59edaf-3067-4ab4-8c8f-cdabf9a648e1/GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 05:50:27,539] [INFO] Task succeeded: fastANI
[2023-06-13 05:50:27,540] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 05:50:27,540] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 05:50:27,542] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 05:50:27,542] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 05:50:27,542] [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 05:50:27,544] [INFO] DFAST Taxonomy check result was written to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-13 05:50:27,544] [INFO] ===== Taxonomy check completed =====
[2023-06-13 05:50:27,545] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 05:50:27,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/checkm_data
[2023-06-13 05:50:27,547] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 05:50:27,585] [INFO] Task started: CheckM
[2023-06-13 05:50:27,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-13 05:50:55,753] [INFO] Task succeeded: CheckM
[2023-06-13 05:50:55,755] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.29%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 05:50:55,780] [INFO] ===== Completeness check finished =====
[2023-06-13 05:50:55,780] [INFO] ===== Start GTDB Search =====
[2023-06-13 05:50:55,781] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-13 05:50:55,781] [INFO] Task started: Blastn
[2023-06-13 05:50:55,781] [INFO] Running command: blastn -query GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgefd7ee0a-367f-45c2-b9f1-0ed437635f65/dqc_reference/reference_markers_gtdb.fasta -out GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 05:50:56,584] [INFO] Task succeeded: Blastn
[2023-06-13 05:50:56,589] [INFO] Selected 19 target genomes.
[2023-06-13 05:50:56,589] [INFO] Target genome list was writen to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 05:50:56,593] [INFO] Task started: fastANI
[2023-06-13 05:50:56,593] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b59edaf-3067-4ab4-8c8f-cdabf9a648e1/GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 05:51:08,979] [INFO] Task succeeded: fastANI
[2023-06-13 05:51:08,995] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 05:51:08,995] [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_002490665.1	s__COE1 sp002490665	95.5896	692	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	95.75	95.74	0.79	0.79	3	conclusive
GCA_910579275.1	s__COE1 sp910579275	85.7883	604	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774345.1	s__COE1 sp009774345	80.6447	351	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.29	99.29	0.85	0.85	2	-
GCA_910578795.1	s__COE1 sp910578795	79.3033	154	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009774245.1	s__COE1 sp009774245	79.0035	344	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.95	99.95	0.99	0.99	2	-
GCA_910588595.1	s__COE1 sp910588595	78.2722	244	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588755.1	s__COE1 sp910588755	78.2533	282	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017622845.1	s__COE1 sp017622845	78.1653	226	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	98.75	98.75	0.86	0.86	2	-
GCA_009774375.1	s__COE1 sp009774375	78.0112	302	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	99.47	99.47	0.88	0.88	2	-
GCA_017391545.1	s__COE1 sp017391545	77.6254	106	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577115.1	s__COE1 sp910577115	77.586	152	805	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__COE1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 05:51:08,997] [INFO] GTDB search result was written to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 05:51:08,997] [INFO] ===== GTDB Search completed =====
[2023-06-13 05:51:09,000] [INFO] DFAST_QC result json was written to GCA_947073535.1_SRR12464015_bin.25_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-13 05:51:09,000] [INFO] DFAST_QC completed!
[2023-06-13 05:51:09,000] [INFO] Total running time: 0h1m7s