[2023-06-13 14:58:47,702] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:58:47,710] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:58:47,710] [INFO] DQC Reference Directory: /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference
[2023-06-13 14:58:49,516] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:58:49,517] [INFO] Task started: Prodigal
[2023-06-13 14:58:49,517] [INFO] Running command: gunzip -c /var/lib/cwl/stgce6a3bb6-765e-4eb5-b0fd-632f4cb3824a/GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:58:55,264] [INFO] Task succeeded: Prodigal
[2023-06-13 14:58:55,264] [INFO] Task started: HMMsearch
[2023-06-13 14:58:55,264] [INFO] Running command: hmmsearch --tblout GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/reference_markers.hmm GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:58:55,488] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:58:55,489] [INFO] Found 6/6 markers.
[2023-06-13 14:58:55,546] [INFO] Query marker FASTA was written to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 14:58:55,546] [INFO] Task started: Blastn
[2023-06-13 14:58:55,546] [INFO] Running command: blastn -query GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/reference_markers.fasta -out GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:58:56,335] [INFO] Task succeeded: Blastn
[2023-06-13 14:58:56,338] [INFO] Selected 25 target genomes.
[2023-06-13 14:58:56,338] [INFO] Target genome list was writen to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 14:58:56,341] [INFO] Task started: fastANI
[2023-06-13 14:58:56,341] [INFO] Running command: fastANI --query /var/lib/cwl/stgce6a3bb6-765e-4eb5-b0fd-632f4cb3824a/GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:59:11,144] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:11,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:59:11,144] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:59:11,153] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 14:59:11,153] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 14:59:11,153] [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
Vescimonas fastidiosa	strain=MM35	GCA_018326305.1	2714353	2714353	type	True	77.6794	66	685	95	below_threshold
Pseudoflavonifractor gallinarum	strain=DSM 107456	GCA_014982855.1	2779352	2779352	type	True	77.1252	79	685	95	below_threshold
Dysosmobacter acutus	strain=MSJ-2	GCA_018919205.1	2841504	2841504	type	True	76.9723	69	685	95	below_threshold
Flavonifractor plautii	strain=JCM 32125	GCA_010508875.1	292800	292800	suspected-type	True	76.8444	84	685	95	below_threshold
Flavonifractor plautii	strain=ATCC 29863	GCA_000239295.1	292800	292800	suspected-type	True	76.835	79	685	95	below_threshold
Dysosmobacter welbionis	strain=J115	GCA_005121165.3	2093857	2093857	type	True	76.7639	72	685	95	below_threshold
Anaerotruncus massiliensis	strain=AT3	GCA_900199635.1	1673720	1673720	type	True	76.3471	65	685	95	below_threshold
Intestinimonas butyriciproducens	strain=SRB-521-5-I	GCA_004154955.1	1297617	1297617	type	True	76.2816	56	685	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_024622565.1	1297617	1297617	type	True	76.2738	55	685	95	below_threshold
Intestinimonas butyriciproducens	strain=DSM 26588	GCA_003096335.1	1297617	1297617	type	True	76.2738	55	685	95	below_threshold
Roseomonas oryzicola	strain=KCTC 22478	GCA_012163135.1	535904	535904	type	True	75.0738	50	685	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:59:11,155] [INFO] DFAST Taxonomy check result was written to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 14:59:11,155] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:59:11,155] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:59:11,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/checkm_data
[2023-06-13 14:59:11,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:59:11,180] [INFO] Task started: CheckM
[2023-06-13 14:59:11,180] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 14:59:32,085] [INFO] Task succeeded: CheckM
[2023-06-13 14:59:32,086] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:59:32,101] [INFO] ===== Completeness check finished =====
[2023-06-13 14:59:32,101] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:59:32,102] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 14:59:32,102] [INFO] Task started: Blastn
[2023-06-13 14:59:32,102] [INFO] Running command: blastn -query GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg29df53a0-ab41-4b1e-a9d9-3b9df4182dcd/dqc_reference/reference_markers_gtdb.fasta -out GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:59:33,405] [INFO] Task succeeded: Blastn
[2023-06-13 14:59:33,408] [INFO] Selected 6 target genomes.
[2023-06-13 14:59:33,409] [INFO] Target genome list was writen to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:59:33,409] [INFO] Task started: fastANI
[2023-06-13 14:59:33,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgce6a3bb6-765e-4eb5-b0fd-632f4cb3824a/GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:59:36,304] [INFO] Task succeeded: fastANI
[2023-06-13 14:59:36,309] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:59:36,309] [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_900757655.1	s__CAG-103 sp900757655	98.0144	557	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.74	95.66	0.88	0.82	7	conclusive
GCA_900317855.1	s__CAG-103 sp900317855	94.5433	532	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	97.11	95.56	0.88	0.84	11	-
GCA_000432375.1	s__CAG-103 sp000432375	93.209	484	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.15	97.87	0.87	0.82	10	-
GCA_900543625.1	s__CAG-103 sp900543625	90.3218	538	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	96.93	95.23	0.89	0.87	12	-
GCA_004556965.1	s__CAG-103 sp004556965	81.2095	335	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	98.49	98.32	0.91	0.88	6	-
GCA_018265835.1	s__CAG-103 sp018265835	81.0888	329	685	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__CAG-103	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 14:59:36,311] [INFO] GTDB search result was written to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 14:59:36,311] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:59:36,314] [INFO] DFAST_QC result json was written to GCA_938005155.1_ERR1600641_bin.106_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 14:59:36,314] [INFO] DFAST_QC completed!
[2023-06-13 14:59:36,314] [INFO] Total running time: 0h0m49s