[2023-06-29 18:14:38,997] [INFO] DFAST_QC pipeline started.
[2023-06-29 18:14:39,004] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 18:14:39,004] [INFO] DQC Reference Directory: /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference
[2023-06-29 18:14:40,451] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 18:14:40,452] [INFO] Task started: Prodigal
[2023-06-29 18:14:40,452] [INFO] Running command: gunzip -c /var/lib/cwl/stge2a924cd-1718-43e2-bc8b-403cc44033bd/GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 18:14:54,926] [INFO] Task succeeded: Prodigal
[2023-06-29 18:14:54,926] [INFO] Task started: HMMsearch
[2023-06-29 18:14:54,926] [INFO] Running command: hmmsearch --tblout GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/reference_markers.hmm GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 18:14:55,221] [INFO] Task succeeded: HMMsearch
[2023-06-29 18:14:55,223] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge2a924cd-1718-43e2-bc8b-403cc44033bd/GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 18:14:55,255] [INFO] Query marker FASTA was written to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 18:14:55,255] [INFO] Task started: Blastn
[2023-06-29 18:14:55,256] [INFO] Running command: blastn -query GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/reference_markers.fasta -out GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:14:55,868] [INFO] Task succeeded: Blastn
[2023-06-29 18:14:55,872] [INFO] Selected 19 target genomes.
[2023-06-29 18:14:55,873] [INFO] Target genome list was writen to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 18:14:55,876] [INFO] Task started: fastANI
[2023-06-29 18:14:55,876] [INFO] Running command: fastANI --query /var/lib/cwl/stge2a924cd-1718-43e2-bc8b-403cc44033bd/GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 18:15:07,463] [INFO] Task succeeded: fastANI
[2023-06-29 18:15:07,464] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 18:15:07,464] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 18:15:07,467] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 18:15:07,467] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 18:15:07,468] [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 18:15:07,472] [INFO] DFAST Taxonomy check result was written to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 18:15:07,473] [INFO] ===== Taxonomy check completed =====
[2023-06-29 18:15:07,473] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 18:15:07,473] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/checkm_data
[2023-06-29 18:15:07,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 18:15:07,512] [INFO] Task started: CheckM
[2023-06-29 18:15:07,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 18:15:53,425] [INFO] Task succeeded: CheckM
[2023-06-29 18:15:53,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 66.35%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 18:15:53,449] [INFO] ===== Completeness check finished =====
[2023-06-29 18:15:53,450] [INFO] ===== Start GTDB Search =====
[2023-06-29 18:15:53,450] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 18:15:53,451] [INFO] Task started: Blastn
[2023-06-29 18:15:53,451] [INFO] Running command: blastn -query GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgba832e7c-ee84-4799-8469-f7aacc33c4c1/dqc_reference/reference_markers_gtdb.fasta -out GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 18:15:54,185] [INFO] Task succeeded: Blastn
[2023-06-29 18:15:54,190] [INFO] Selected 13 target genomes.
[2023-06-29 18:15:54,190] [INFO] Target genome list was writen to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 18:15:54,198] [INFO] Task started: fastANI
[2023-06-29 18:15:54,198] [INFO] Running command: fastANI --query /var/lib/cwl/stge2a924cd-1718-43e2-bc8b-403cc44033bd/GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 18:16:01,021] [INFO] Task succeeded: fastANI
[2023-06-29 18:16:01,039] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 18:16:01,039] [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_015060395.1	s__Cryptobacteroides sp015060395	97.8245	714	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.90	97.87	0.88	0.85	4	conclusive
GCA_017626555.1	s__Cryptobacteroides sp017626555	84.482	500	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017465225.1	s__Cryptobacteroides sp017465225	82.0158	359	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	97.02	96.60	0.67	0.61	4	-
GCA_017437125.1	s__Cryptobacteroides sp017437125	80.4993	405	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017630215.1	s__Cryptobacteroides sp017630215	80.382	284	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017561265.1	s__Cryptobacteroides sp017561265	80.0098	260	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017556765.1	s__Cryptobacteroides sp017556765	79.9616	227	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017546585.1	s__Cryptobacteroides sp017546585	79.4827	260	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550025.1	s__Cryptobacteroides sp017550025	79.4279	289	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017472115.1	s__Cryptobacteroides sp017472115	79.3236	192	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017626355.1	s__Cryptobacteroides sp017626355	79.2085	198	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017559545.1	s__Cryptobacteroides sp017559545	78.2495	151	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017474265.1	s__Cryptobacteroides sp017474265	77.7958	207	896	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA932;g__Cryptobacteroides	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 18:16:01,041] [INFO] GTDB search result was written to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 18:16:01,042] [INFO] ===== GTDB Search completed =====
[2023-06-29 18:16:01,045] [INFO] DFAST_QC result json was written to GCA_937892205.1_SRR6425826_bin.12_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 18:16:01,045] [INFO] DFAST_QC completed!
[2023-06-29 18:16:01,045] [INFO] Total running time: 0h1m22s