[2023-06-17 18:33:44,146] [INFO] DFAST_QC pipeline started.
[2023-06-17 18:33:44,151] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 18:33:44,151] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference
[2023-06-17 18:33:45,891] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 18:33:45,892] [INFO] Task started: Prodigal
[2023-06-17 18:33:45,893] [INFO] Running command: gunzip -c /var/lib/cwl/stgc04b0156-b414-4cf1-9d51-a2463936f68c/GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna.gz | prodigal -d GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/cds.fna -a GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 18:33:53,402] [INFO] Task succeeded: Prodigal
[2023-06-17 18:33:53,403] [INFO] Task started: HMMsearch
[2023-06-17 18:33:53,403] [INFO] Running command: hmmsearch --tblout GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/reference_markers.hmm GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/protein.faa > /dev/null
[2023-06-17 18:33:53,669] [INFO] Task succeeded: HMMsearch
[2023-06-17 18:33:53,672] [INFO] Found 6/6 markers.
[2023-06-17 18:33:53,695] [INFO] Query marker FASTA was written to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/markers.fasta
[2023-06-17 18:33:53,696] [INFO] Task started: Blastn
[2023-06-17 18:33:53,696] [INFO] Running command: blastn -query GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/reference_markers.fasta -out GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:33:54,415] [INFO] Task succeeded: Blastn
[2023-06-17 18:33:54,420] [INFO] Selected 25 target genomes.
[2023-06-17 18:33:54,420] [INFO] Target genome list was writen to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/target_genomes.txt
[2023-06-17 18:33:54,424] [INFO] Task started: fastANI
[2023-06-17 18:33:54,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04b0156-b414-4cf1-9d51-a2463936f68c/GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna.gz --refList GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/target_genomes.txt --output GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 18:34:11,609] [INFO] Task succeeded: fastANI
[2023-06-17 18:34:11,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 18:34:11,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 18:34:11,619] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 18:34:11,619] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 18:34:11,619] [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
Clostridium jeddahense	strain=JCD	GCA_000577335.1	1414721	1414721	type	True	77.1693	54	814	95	below_threshold
Anaeromassilibacillus senegalensis	strain=mt9	GCA_001261775.1	1673717	1673717	type	True	76.6528	75	814	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 18:34:11,621] [INFO] DFAST Taxonomy check result was written to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/tc_result.tsv
[2023-06-17 18:34:11,622] [INFO] ===== Taxonomy check completed =====
[2023-06-17 18:34:11,622] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 18:34:11,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/checkm_data
[2023-06-17 18:34:11,624] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 18:34:11,656] [INFO] Task started: CheckM
[2023-06-17 18:34:11,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/checkm_input GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/checkm_result
[2023-06-17 18:34:39,273] [INFO] Task succeeded: CheckM
[2023-06-17 18:34:39,274] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 18:34:39,297] [INFO] ===== Completeness check finished =====
[2023-06-17 18:34:39,297] [INFO] ===== Start GTDB Search =====
[2023-06-17 18:34:39,298] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/markers.fasta)
[2023-06-17 18:34:39,298] [INFO] Task started: Blastn
[2023-06-17 18:34:39,298] [INFO] Running command: blastn -query GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f7d809-db4f-4acc-81d4-32d78cfd17a5/dqc_reference/reference_markers_gtdb.fasta -out GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 18:34:40,430] [INFO] Task succeeded: Blastn
[2023-06-17 18:34:40,435] [INFO] Selected 8 target genomes.
[2023-06-17 18:34:40,436] [INFO] Target genome list was writen to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 18:34:40,442] [INFO] Task started: fastANI
[2023-06-17 18:34:40,442] [INFO] Running command: fastANI --query /var/lib/cwl/stgc04b0156-b414-4cf1-9d51-a2463936f68c/GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna.gz --refList GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/target_genomes_gtdb.txt --output GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 18:34:44,544] [INFO] Task succeeded: fastANI
[2023-06-17 18:34:44,558] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 18:34:44,558] [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_008681155.1	s__UBA1417 sp003531055	97.5663	703	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	97.97	97.38	0.92	0.84	13	conclusive
GCA_004555625.1	s__UBA1417 sp004555625	80.1702	353	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900549945.1	s__UBA1417 sp900549945	79.7227	268	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.46	97.65	0.85	0.74	4	-
GCA_900552925.1	s__UBA1417 sp900552925	79.6186	242	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.06	97.73	0.91	0.83	5	-
GCA_017407665.1	s__UBA1417 sp017407665	78.9055	230	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002305575.1	s__UBA1417 sp002305575	78.7971	298	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	98.68	98.68	0.86	0.86	2	-
GCA_017623855.1	s__UBA1417 sp017623855	78.2976	176	814	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__UBA1417	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 18:34:44,561] [INFO] GTDB search result was written to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/result_gtdb.tsv
[2023-06-17 18:34:44,561] [INFO] ===== GTDB Search completed =====
[2023-06-17 18:34:44,564] [INFO] DFAST_QC result json was written to GCA_905200205.1_SRR7721898-mag-bin.66_genomic.fna/dqc_result.json
[2023-06-17 18:34:44,564] [INFO] DFAST_QC completed!
[2023-06-17 18:34:44,564] [INFO] Total running time: 0h1m0s