[2023-06-13 02:18:17,885] [INFO] DFAST_QC pipeline started.
[2023-06-13 02:18:17,905] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 02:18:17,905] [INFO] DQC Reference Directory: /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference
[2023-06-13 02:18:19,225] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 02:18:19,226] [INFO] Task started: Prodigal
[2023-06-13 02:18:19,226] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fd0d8d5-9df0-43ed-bb8c-53e2280b7819/GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 02:18:25,195] [INFO] Task succeeded: Prodigal
[2023-06-13 02:18:25,196] [INFO] Task started: HMMsearch
[2023-06-13 02:18:25,196] [INFO] Running command: hmmsearch --tblout GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/reference_markers.hmm GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 02:18:25,466] [INFO] Task succeeded: HMMsearch
[2023-06-13 02:18:25,468] [INFO] Found 6/6 markers.
[2023-06-13 02:18:25,501] [INFO] Query marker FASTA was written to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 02:18:25,502] [INFO] Task started: Blastn
[2023-06-13 02:18:25,502] [INFO] Running command: blastn -query GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/reference_markers.fasta -out GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:18:26,140] [INFO] Task succeeded: Blastn
[2023-06-13 02:18:26,145] [INFO] Selected 35 target genomes.
[2023-06-13 02:18:26,146] [INFO] Target genome list was writen to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 02:18:26,153] [INFO] Task started: fastANI
[2023-06-13 02:18:26,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fd0d8d5-9df0-43ed-bb8c-53e2280b7819/GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 02:18:49,760] [INFO] Task succeeded: fastANI
[2023-06-13 02:18:49,760] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 02:18:49,761] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 02:18:49,767] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 02:18:49,768] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 02:18:49,768] [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
Pradoshia eiseniae	strain=EAG3	GCA_002946355.1	2064768	2064768	type	True	82.5161	363	480	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 02:18:49,771] [INFO] DFAST Taxonomy check result was written to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 02:18:49,772] [INFO] ===== Taxonomy check completed =====
[2023-06-13 02:18:49,772] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 02:18:49,772] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/checkm_data
[2023-06-13 02:18:49,773] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 02:18:49,819] [INFO] Task started: CheckM
[2023-06-13 02:18:49,819] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 02:19:14,900] [INFO] Task succeeded: CheckM
[2023-06-13 02:19:14,902] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.02%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 02:19:14,924] [INFO] ===== Completeness check finished =====
[2023-06-13 02:19:14,925] [INFO] ===== Start GTDB Search =====
[2023-06-13 02:19:14,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 02:19:14,925] [INFO] Task started: Blastn
[2023-06-13 02:19:14,926] [INFO] Running command: blastn -query GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga2760d79-1a07-48a8-a742-70ced6ae5d89/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 02:19:15,889] [INFO] Task succeeded: Blastn
[2023-06-13 02:19:15,893] [INFO] Selected 24 target genomes.
[2023-06-13 02:19:15,893] [INFO] Target genome list was writen to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 02:19:15,959] [INFO] Task started: fastANI
[2023-06-13 02:19:15,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fd0d8d5-9df0-43ed-bb8c-53e2280b7819/GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 02:19:31,706] [INFO] Task succeeded: fastANI
[2023-06-13 02:19:31,715] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 02:19:31,716] [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
GCF_001183965.1	s__Pradoshia sp001183965	98.7568	468	480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002946355.1	s__Pradoshia eiseniae	82.5161	363	480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904501845.1	s__Pradoshia sp904501845	82.4687	305	480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	100.00	100.00	0.98	0.98	2	-
GCF_008935075.1	s__Pradoshia sp001685035	78.8868	113	480	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-1321;g__Pradoshia	95.0	99.44	99.12	0.97	0.95	4	-
--------------------------------------------------------------------------------
[2023-06-13 02:19:31,718] [INFO] GTDB search result was written to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 02:19:31,719] [INFO] ===== GTDB Search completed =====
[2023-06-13 02:19:31,722] [INFO] DFAST_QC result json was written to GCA_938005495.1_ERR912050_bin.68_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 02:19:31,722] [INFO] DFAST_QC completed!
[2023-06-13 02:19:31,722] [INFO] Total running time: 0h1m14s