[2023-06-29 13:25:10,715] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:25:10,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:25:10,717] [INFO] DQC Reference Directory: /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference
[2023-06-29 13:25:12,707] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:25:12,708] [INFO] Task started: Prodigal
[2023-06-29 13:25:12,709] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a08c458-c616-4d7c-ad4a-e6cb1162a63e/GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:25:18,327] [INFO] Task succeeded: Prodigal
[2023-06-29 13:25:18,327] [INFO] Task started: HMMsearch
[2023-06-29 13:25:18,327] [INFO] Running command: hmmsearch --tblout GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/reference_markers.hmm GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:25:18,593] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:25:18,594] [INFO] Found 6/6 markers.
[2023-06-29 13:25:18,624] [INFO] Query marker FASTA was written to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:25:18,624] [INFO] Task started: Blastn
[2023-06-29 13:25:18,624] [INFO] Running command: blastn -query GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/reference_markers.fasta -out GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:25:19,230] [INFO] Task succeeded: Blastn
[2023-06-29 13:25:19,235] [INFO] Selected 5 target genomes.
[2023-06-29 13:25:19,236] [INFO] Target genome list was writen to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:25:19,237] [INFO] Task started: fastANI
[2023-06-29 13:25:19,237] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a08c458-c616-4d7c-ad4a-e6cb1162a63e/GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:25:22,035] [INFO] Task succeeded: fastANI
[2023-06-29 13:25:22,036] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:25:22,036] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:25:22,048] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:25:22,048] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:25:22,049] [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
Megasphaera elsdenii	strain=DSM 20460	GCA_000283495.2	907	907	type	True	90.4183	487	609	95	below_threshold
Megasphaera elsdenii	strain=ATCC 25940	GCA_003010495.1	907	907	type	True	90.299	490	609	95	below_threshold
Megasphaera massiliensis	strain=NP3	GCA_000455225.1	1232428	1232428	suspected-type	True	82.5007	388	609	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003367905.1	2144175	2144175	type	True	79.6039	279	609	95	below_threshold
Megasphaera stantonii	strain=AJH120	GCA_003030445.1	2144175	2144175	type	True	79.5729	279	609	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:25:22,051] [INFO] DFAST Taxonomy check result was written to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:25:22,052] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:25:22,052] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:25:22,053] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/checkm_data
[2023-06-29 13:25:22,055] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:25:22,087] [INFO] Task started: CheckM
[2023-06-29 13:25:22,087] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:25:44,879] [INFO] Task succeeded: CheckM
[2023-06-29 13:25:44,887] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:25:44,909] [INFO] ===== Completeness check finished =====
[2023-06-29 13:25:44,910] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:25:44,910] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:25:44,911] [INFO] Task started: Blastn
[2023-06-29 13:25:44,911] [INFO] Running command: blastn -query GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg35be995e-7f59-4847-b5ca-d82094dc07bd/dqc_reference/reference_markers_gtdb.fasta -out GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:25:45,800] [INFO] Task succeeded: Blastn
[2023-06-29 13:25:45,804] [INFO] Selected 7 target genomes.
[2023-06-29 13:25:45,805] [INFO] Target genome list was writen to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:25:45,806] [INFO] Task started: fastANI
[2023-06-29 13:25:45,807] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a08c458-c616-4d7c-ad4a-e6cb1162a63e/GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:25:50,052] [INFO] Task succeeded: fastANI
[2023-06-29 13:25:50,060] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:25:50,060] [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
GCF_000417505.1	s__Megasphaera sp000417505	94.4171	482	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.18	97.65	0.90	0.81	11	-
GCA_902388315.1	s__Megasphaera sp902388315	91.567	383	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.43	99.12	0.87	0.82	3	-
GCF_003010495.1	s__Megasphaera elsdenii	90.3311	489	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.27	97.55	0.90	0.81	29	-
GCA_900548635.1	s__Megasphaera sp900548635	86.8891	354	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.28	98.56	0.89	0.79	3	-
GCF_001546855.1	s__Megasphaera sp001546855	82.7569	394	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	99.96	99.94	0.97	0.94	9	-
GCA_900539295.1	s__Megasphaera sp900539295	82.6378	385	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002319965.1	s__Megasphaera sp002319965	82.532	308	609	d__Bacteria;p__Firmicutes_C;c__Negativicutes;o__Veillonellales;f__Megasphaeraceae;g__Megasphaera	95.0	98.41	98.03	0.89	0.89	4	-
--------------------------------------------------------------------------------
[2023-06-29 13:25:50,062] [INFO] GTDB search result was written to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:25:50,064] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:25:50,069] [INFO] DFAST_QC result json was written to GCA_937968145.1_SRR7658643_bin.17_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:25:50,069] [INFO] DFAST_QC completed!
[2023-06-29 13:25:50,069] [INFO] Total running time: 0h0m39s