[2023-06-14 01:32:49,733] [INFO] DFAST_QC pipeline started.
[2023-06-14 01:32:49,735] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 01:32:49,735] [INFO] DQC Reference Directory: /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference
[2023-06-14 01:32:52,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 01:32:52,044] [INFO] Task started: Prodigal
[2023-06-14 01:32:52,045] [INFO] Running command: gunzip -c /var/lib/cwl/stg76e69272-d061-40ad-9c2f-b7a3e11d4b9d/GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 01:32:56,802] [INFO] Task succeeded: Prodigal
[2023-06-14 01:32:56,803] [INFO] Task started: HMMsearch
[2023-06-14 01:32:56,803] [INFO] Running command: hmmsearch --tblout GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/reference_markers.hmm GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-14 01:32:57,057] [INFO] Task succeeded: HMMsearch
[2023-06-14 01:32:57,059] [INFO] Found 6/6 markers.
[2023-06-14 01:32:57,082] [INFO] Query marker FASTA was written to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-14 01:32:57,083] [INFO] Task started: Blastn
[2023-06-14 01:32:57,083] [INFO] Running command: blastn -query GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/reference_markers.fasta -out GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:32:57,712] [INFO] Task succeeded: Blastn
[2023-06-14 01:32:57,715] [INFO] Selected 17 target genomes.
[2023-06-14 01:32:57,716] [INFO] Target genome list was writen to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-14 01:32:57,722] [INFO] Task started: fastANI
[2023-06-14 01:32:57,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e69272-d061-40ad-9c2f-b7a3e11d4b9d/GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 01:33:08,383] [INFO] Task succeeded: fastANI
[2023-06-14 01:33:08,384] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 01:33:08,384] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 01:33:08,386] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-14 01:33:08,386] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-14 01:33:08,386] [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
--------------------------------------------------------------------------------
[2023-06-14 01:33:08,388] [INFO] DFAST Taxonomy check result was written to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-14 01:33:08,389] [INFO] ===== Taxonomy check completed =====
[2023-06-14 01:33:08,389] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 01:33:08,389] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/checkm_data
[2023-06-14 01:33:08,391] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 01:33:08,417] [INFO] Task started: CheckM
[2023-06-14 01:33:08,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-14 01:33:29,109] [INFO] Task succeeded: CheckM
[2023-06-14 01:33:29,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 01:33:29,131] [INFO] ===== Completeness check finished =====
[2023-06-14 01:33:29,131] [INFO] ===== Start GTDB Search =====
[2023-06-14 01:33:29,132] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-14 01:33:29,132] [INFO] Task started: Blastn
[2023-06-14 01:33:29,132] [INFO] Running command: blastn -query GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg200ee157-e998-4929-a0a7-e878af431eb8/dqc_reference/reference_markers_gtdb.fasta -out GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 01:33:30,137] [INFO] Task succeeded: Blastn
[2023-06-14 01:33:30,142] [INFO] Selected 16 target genomes.
[2023-06-14 01:33:30,142] [INFO] Target genome list was writen to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 01:33:30,159] [INFO] Task started: fastANI
[2023-06-14 01:33:30,159] [INFO] Running command: fastANI --query /var/lib/cwl/stg76e69272-d061-40ad-9c2f-b7a3e11d4b9d/GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 01:33:36,050] [INFO] Task succeeded: fastANI
[2023-06-14 01:33:36,056] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 01:33:36,056] [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_003524145.1	s__CAG-724 sp003524145	98.2894	486	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	98.59	98.21	0.88	0.83	6	conclusive
GCA_905202255.1	s__CAG-724 sp905202255	94.9545	464	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551005.1	s__CAG-724 sp900551005	81.6734	351	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-724	95.0	99.35	98.70	0.93	0.88	3	-
GCA_900544285.1	s__CAG-841 sp900544285	80.281	81	611	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__CAG-272;g__CAG-841	95.0	98.87	98.45	0.89	0.88	4	-
--------------------------------------------------------------------------------
[2023-06-14 01:33:36,058] [INFO] GTDB search result was written to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-14 01:33:36,059] [INFO] ===== GTDB Search completed =====
[2023-06-14 01:33:36,061] [INFO] DFAST_QC result json was written to GCA_938031155.1_ERR1430485_bin.16_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-14 01:33:36,061] [INFO] DFAST_QC completed!
[2023-06-14 01:33:36,061] [INFO] Total running time: 0h0m46s