[2023-06-12 23:05:59,659] [INFO] DFAST_QC pipeline started.
[2023-06-12 23:05:59,662] [INFO] DFAST_QC version: 0.5.7
[2023-06-12 23:05:59,662] [INFO] DQC Reference Directory: /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference
[2023-06-12 23:06:01,033] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-12 23:06:01,034] [INFO] Task started: Prodigal
[2023-06-12 23:06:01,035] [INFO] Running command: gunzip -c /var/lib/cwl/stgd61f8b45-ed0a-4ddd-870a-19da4baf449e/GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-12 23:06:02,898] [INFO] Task succeeded: Prodigal
[2023-06-12 23:06:02,898] [INFO] Task started: HMMsearch
[2023-06-12 23:06:02,898] [INFO] Running command: hmmsearch --tblout GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/reference_markers.hmm GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-12 23:06:03,125] [INFO] Task succeeded: HMMsearch
[2023-06-12 23:06:03,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd61f8b45-ed0a-4ddd-870a-19da4baf449e/GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-12 23:06:03,150] [INFO] Query marker FASTA was written to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-12 23:06:03,151] [INFO] Task started: Blastn
[2023-06-12 23:06:03,151] [INFO] Running command: blastn -query GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/reference_markers.fasta -out GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:03,768] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:03,773] [INFO] Selected 25 target genomes.
[2023-06-12 23:06:03,773] [INFO] Target genome list was writen to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-12 23:06:03,780] [INFO] Task started: fastANI
[2023-06-12 23:06:03,780] [INFO] Running command: fastANI --query /var/lib/cwl/stgd61f8b45-ed0a-4ddd-870a-19da4baf449e/GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-12 23:06:14,977] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:14,978] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-12 23:06:14,978] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-12 23:06:14,985] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-12 23:06:14,985] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-12 23:06:14,985] [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 puniceum	strain=DSM 2619	GCA_002006345.1	29367	29367	type	True	74.733	55	417	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-12 23:06:14,988] [INFO] DFAST Taxonomy check result was written to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-12 23:06:14,989] [INFO] ===== Taxonomy check completed =====
[2023-06-12 23:06:14,989] [INFO] ===== Start completeness check using CheckM =====
[2023-06-12 23:06:14,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/checkm_data
[2023-06-12 23:06:14,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-12 23:06:15,011] [INFO] Task started: CheckM
[2023-06-12 23:06:15,012] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-12 23:06:29,157] [INFO] Task succeeded: CheckM
[2023-06-12 23:06:29,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-12 23:06:29,181] [INFO] ===== Completeness check finished =====
[2023-06-12 23:06:29,181] [INFO] ===== Start GTDB Search =====
[2023-06-12 23:06:29,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-12 23:06:29,182] [INFO] Task started: Blastn
[2023-06-12 23:06:29,182] [INFO] Running command: blastn -query GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg71478ad1-9e77-4b53-a471-cc5bcdb4a084/dqc_reference/reference_markers_gtdb.fasta -out GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-12 23:06:30,014] [INFO] Task succeeded: Blastn
[2023-06-12 23:06:30,018] [INFO] Selected 13 target genomes.
[2023-06-12 23:06:30,019] [INFO] Target genome list was writen to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-12 23:06:30,024] [INFO] Task started: fastANI
[2023-06-12 23:06:30,025] [INFO] Running command: fastANI --query /var/lib/cwl/stgd61f8b45-ed0a-4ddd-870a-19da4baf449e/GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-12 23:06:33,021] [INFO] Task succeeded: fastANI
[2023-06-12 23:06:33,043] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-12 23:06:33,043] [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_000433675.1	s__CAG-433 sp000433675	99.4403	395	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	97.55	95.67	0.87	0.75	5	conclusive
GCA_900546245.1	s__CAG-433 sp900546245	92.2145	272	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	97.58	97.10	0.81	0.77	4	-
GCA_017938725.1	s__CAG-433 sp017938725	79.7194	177	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017634385.1	s__CAG-433 sp017634385	79.1516	129	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017459965.1	s__CAG-433 sp017459965	78.8577	172	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320735.1	s__CAG-433 sp900320735	78.0104	121	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-433	95.0	100.00	100.00	1.00	1.00	2	-
GCA_016290885.1	s__RUG13038 sp016290885	77.5895	84	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418945.1	s__RUG13038 sp017418945	77.5301	85	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017627015.1	s__RUG13038 sp017627015	76.8386	83	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG13038	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017936845.1	s__UBA5026 sp017936845	76.2107	78	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5026	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017410525.1	s__UMGS1613 sp017410525	75.9537	58	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UMGS1613	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902795975.1	s__UBA5578 sp902795975	75.4485	69	417	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__UBA5578	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-12 23:06:33,046] [INFO] GTDB search result was written to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-12 23:06:33,046] [INFO] ===== GTDB Search completed =====
[2023-06-12 23:06:33,050] [INFO] DFAST_QC result json was written to GCA_938044265.1_SRR7721868_bin.44_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-12 23:06:33,050] [INFO] DFAST_QC completed!
[2023-06-12 23:06:33,050] [INFO] Total running time: 0h0m33s