[2023-06-13 04:36:23,494] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:36:23,497] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:36:23,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference
[2023-06-13 04:36:25,311] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:36:25,313] [INFO] Task started: Prodigal
[2023-06-13 04:36:25,313] [INFO] Running command: gunzip -c /var/lib/cwl/stgb19a124c-e50f-4c78-b78d-1c7a3c2fde38/GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:36:28,250] [INFO] Task succeeded: Prodigal
[2023-06-13 04:36:28,251] [INFO] Task started: HMMsearch
[2023-06-13 04:36:28,251] [INFO] Running command: hmmsearch --tblout GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/reference_markers.hmm GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:36:28,487] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:36:28,489] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgb19a124c-e50f-4c78-b78d-1c7a3c2fde38/GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-13 04:36:28,519] [INFO] Query marker FASTA was written to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 04:36:28,520] [INFO] Task started: Blastn
[2023-06-13 04:36:28,520] [INFO] Running command: blastn -query GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/reference_markers.fasta -out GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:29,135] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:29,140] [INFO] Selected 25 target genomes.
[2023-06-13 04:36:29,141] [INFO] Target genome list was writen to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 04:36:29,176] [INFO] Task started: fastANI
[2023-06-13 04:36:29,176] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19a124c-e50f-4c78-b78d-1c7a3c2fde38/GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:36:38,881] [INFO] Task succeeded: fastANI
[2023-06-13 04:36:38,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:36:38,883] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:36:38,885] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:36:38,885] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 04:36:38,886] [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 04:36:38,888] [INFO] DFAST Taxonomy check result was written to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 04:36:38,888] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:36:38,889] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:36:38,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/checkm_data
[2023-06-13 04:36:38,892] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:36:38,920] [INFO] Task started: CheckM
[2023-06-13 04:36:38,921] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 04:36:57,202] [INFO] Task succeeded: CheckM
[2023-06-13 04:36:57,204] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 15.61%
Strain heterogeneity: 5.88%
--------------------------------------------------------------------------------
[2023-06-13 04:36:57,253] [INFO] ===== Completeness check finished =====
[2023-06-13 04:36:57,254] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:36:57,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 04:36:57,254] [INFO] Task started: Blastn
[2023-06-13 04:36:57,254] [INFO] Running command: blastn -query GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg21a1b2b6-12e7-44c5-99d3-7aa89140174b/dqc_reference/reference_markers_gtdb.fasta -out GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:36:58,124] [INFO] Task succeeded: Blastn
[2023-06-13 04:36:58,129] [INFO] Selected 12 target genomes.
[2023-06-13 04:36:58,130] [INFO] Target genome list was writen to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:36:58,138] [INFO] Task started: fastANI
[2023-06-13 04:36:58,139] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19a124c-e50f-4c78-b78d-1c7a3c2fde38/GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:37:01,461] [INFO] Task succeeded: fastANI
[2023-06-13 04:37:01,467] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:37:01,467] [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_000432895.1	s__CAG-449 sp000432895	98.4631	500	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449	95.0	98.56	98.56	0.83	0.83	2	conclusive
GCA_900551385.1	s__CAG-449 sp900551385	80.8801	171	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449	95.0	95.57	95.00	0.71	0.63	3	-
GCA_905204225.1	s__CAG-449 sp905204225	80.733	221	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__CAG-449	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059095.1	s__UBA3210 sp015059095	77.2794	86	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__UBA3210	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015059045.1	s__UBA3210 sp015059045	76.8162	73	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-449;g__UBA3210	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017450215.1	s__RGIG3506 sp017450215	75.0914	54	646	d__Bacteria;p__Firmicutes;c__Bacilli;o__ML615J-28;f__CAG-698;g__RGIG3506	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 04:37:01,470] [INFO] GTDB search result was written to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 04:37:01,470] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:37:01,473] [INFO] DFAST_QC result json was written to GCA_938039255.1_ERR505083_bin.20_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 04:37:01,473] [INFO] DFAST_QC completed!
[2023-06-13 04:37:01,473] [INFO] Total running time: 0h0m38s