[2023-06-29 15:33:48,820] [INFO] DFAST_QC pipeline started.
[2023-06-29 15:33:48,823] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 15:33:48,824] [INFO] DQC Reference Directory: /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference
[2023-06-29 15:33:50,222] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 15:33:50,240] [INFO] Task started: Prodigal
[2023-06-29 15:33:50,241] [INFO] Running command: gunzip -c /var/lib/cwl/stgc011033d-556b-412d-8d80-6f679b09f1f5/GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 15:33:56,841] [INFO] Task succeeded: Prodigal
[2023-06-29 15:33:56,841] [INFO] Task started: HMMsearch
[2023-06-29 15:33:56,841] [INFO] Running command: hmmsearch --tblout GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/reference_markers.hmm GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 15:33:57,118] [INFO] Task succeeded: HMMsearch
[2023-06-29 15:33:57,119] [INFO] Found 6/6 markers.
[2023-06-29 15:33:57,149] [INFO] Query marker FASTA was written to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 15:33:57,150] [INFO] Task started: Blastn
[2023-06-29 15:33:57,150] [INFO] Running command: blastn -query GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/reference_markers.fasta -out GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:33:57,832] [INFO] Task succeeded: Blastn
[2023-06-29 15:33:57,836] [INFO] Selected 33 target genomes.
[2023-06-29 15:33:57,836] [INFO] Target genome list was writen to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 15:33:57,838] [INFO] Task started: fastANI
[2023-06-29 15:33:57,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgc011033d-556b-412d-8d80-6f679b09f1f5/GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 15:34:15,542] [INFO] Task succeeded: fastANI
[2023-06-29 15:34:15,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 15:34:15,543] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 15:34:15,544] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 15:34:15,544] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 15:34:15,544] [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
--------------------------------------------------------------------------------
[2023-06-29 15:34:15,546] [INFO] DFAST Taxonomy check result was written to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 15:34:15,547] [INFO] ===== Taxonomy check completed =====
[2023-06-29 15:34:15,547] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 15:34:15,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/checkm_data
[2023-06-29 15:34:15,550] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 15:34:15,590] [INFO] Task started: CheckM
[2023-06-29 15:34:15,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 15:34:42,309] [INFO] Task succeeded: CheckM
[2023-06-29 15:34:42,311] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 15:34:42,334] [INFO] ===== Completeness check finished =====
[2023-06-29 15:34:42,335] [INFO] ===== Start GTDB Search =====
[2023-06-29 15:34:42,335] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 15:34:42,336] [INFO] Task started: Blastn
[2023-06-29 15:34:42,336] [INFO] Running command: blastn -query GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg181eb15d-0a18-422e-b47b-446c3b174450/dqc_reference/reference_markers_gtdb.fasta -out GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 15:34:43,369] [INFO] Task succeeded: Blastn
[2023-06-29 15:34:43,374] [INFO] Selected 21 target genomes.
[2023-06-29 15:34:43,375] [INFO] Target genome list was writen to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 15:34:43,380] [INFO] Task started: fastANI
[2023-06-29 15:34:43,380] [INFO] Running command: fastANI --query /var/lib/cwl/stgc011033d-556b-412d-8d80-6f679b09f1f5/GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 15:34:54,276] [INFO] Task succeeded: fastANI
[2023-06-29 15:34:54,286] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 15:34:54,286] [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_910577835.1	s__CAG-303 sp910577835	99.0467	875	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910585215.1	s__CAG-303 sp910585215	88.0707	814	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000437755.1	s__CAG-303 sp000437755	77.6353	199	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	98.21	98.19	0.88	0.88	3	-
GCA_902797675.1	s__CAG-303 sp902797675	76.8649	88	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539455.1	s__CAG-303 sp900539455	76.3629	59	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-303	95.0	99.77	99.53	0.98	0.96	3	-
GCF_014287955.1	s__Lachnospira sp900316325	76.0217	54	1005	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnospira	95.0	98.86	98.35	0.93	0.88	10	-
--------------------------------------------------------------------------------
[2023-06-29 15:34:54,289] [INFO] GTDB search result was written to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 15:34:54,289] [INFO] ===== GTDB Search completed =====
[2023-06-29 15:34:54,292] [INFO] DFAST_QC result json was written to GCA_937877475.1_SRR5574493_bin.105_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 15:34:54,292] [INFO] DFAST_QC completed!
[2023-06-29 15:34:54,292] [INFO] Total running time: 0h1m5s