[2023-06-29 22:10:51,336] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:10:51,344] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:10:51,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference
[2023-06-29 22:10:52,678] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:10:52,679] [INFO] Task started: Prodigal
[2023-06-29 22:10:52,679] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfcdbb55-0ce2-435c-a698-c05d6580287a/GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna.gz | prodigal -d GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/cds.fna -a GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:11:01,904] [INFO] Task succeeded: Prodigal
[2023-06-29 22:11:01,905] [INFO] Task started: HMMsearch
[2023-06-29 22:11:01,905] [INFO] Running command: hmmsearch --tblout GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/reference_markers.hmm GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:11:02,137] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:11:02,139] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfcdbb55-0ce2-435c-a698-c05d6580287a/GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna.gz]
[2023-06-29 22:11:02,164] [INFO] Query marker FASTA was written to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/markers.fasta
[2023-06-29 22:11:02,164] [INFO] Task started: Blastn
[2023-06-29 22:11:02,164] [INFO] Running command: blastn -query GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/reference_markers.fasta -out GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:11:02,657] [INFO] Task succeeded: Blastn
[2023-06-29 22:11:02,661] [INFO] Selected 7 target genomes.
[2023-06-29 22:11:02,661] [INFO] Target genome list was writen to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/target_genomes.txt
[2023-06-29 22:11:02,662] [INFO] Task started: fastANI
[2023-06-29 22:11:02,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfcdbb55-0ce2-435c-a698-c05d6580287a/GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna.gz --refList GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/target_genomes.txt --output GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:11:05,739] [INFO] Task succeeded: fastANI
[2023-06-29 22:11:05,739] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:11:05,740] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:11:05,749] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:11:05,749] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:11:05,749] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	78.5167	204	517	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.6255	177	517	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	76.9896	88	517	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	76.6595	79	517	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:11:05,752] [INFO] DFAST Taxonomy check result was written to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/tc_result.tsv
[2023-06-29 22:11:05,752] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:11:05,753] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:11:05,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/checkm_data
[2023-06-29 22:11:05,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:11:05,781] [INFO] Task started: CheckM
[2023-06-29 22:11:05,782] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/checkm_input GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/checkm_result
[2023-06-29 22:11:39,112] [INFO] Task succeeded: CheckM
[2023-06-29 22:11:39,114] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 22:11:39,136] [INFO] ===== Completeness check finished =====
[2023-06-29 22:11:39,137] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:11:39,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/markers.fasta)
[2023-06-29 22:11:39,138] [INFO] Task started: Blastn
[2023-06-29 22:11:39,138] [INFO] Running command: blastn -query GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/markers.fasta -db /var/lib/cwl/stg92c06cf3-5e5b-447f-9b7e-27453a75d0d8/dqc_reference/reference_markers_gtdb.fasta -out GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:11:39,594] [INFO] Task succeeded: Blastn
[2023-06-29 22:11:39,599] [INFO] Selected 8 target genomes.
[2023-06-29 22:11:39,599] [INFO] Target genome list was writen to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:11:39,600] [INFO] Task started: fastANI
[2023-06-29 22:11:39,601] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfcdbb55-0ce2-435c-a698-c05d6580287a/GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna.gz --refList GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/target_genomes_gtdb.txt --output GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:11:43,628] [INFO] Task succeeded: fastANI
[2023-06-29 22:11:43,638] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:11:43,638] [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_005843825.1	s__Chlorobium sp005843825	98.3829	468	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.19	97.55	0.89	0.82	50	conclusive
GCA_903851385.1	s__Chlorobium sp903851385	90.4204	461	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.86	99.82	0.97	0.97	3	-
GCA_903920215.1	s__Chlorobium sp903920215	90.2436	432	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903908555.1	s__Chlorobium sp903908555	89.1107	364	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.53	0.79	0.79	2	-
GCA_903895195.1	s__Chlorobium sp903895195	87.1353	441	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.65	0.92	0.86	65	-
GCA_903904495.1	s__Chlorobium sp903904495	83.9469	315	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.87	98.87	0.74	0.74	2	-
GCA_903940125.1	s__Chlorobium sp903940125	83.0321	404	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.50	97.06	0.88	0.72	14	-
GCA_012972825.1	s__Chlorobium sp012972825	82.5821	390	517	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 22:11:43,640] [INFO] GTDB search result was written to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/result_gtdb.tsv
[2023-06-29 22:11:43,641] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:11:43,644] [INFO] DFAST_QC result json was written to GCA_903832405.1_freshwater_MAG_---_MJ130702B_bin-240_genomic.fna/dqc_result.json
[2023-06-29 22:11:43,644] [INFO] DFAST_QC completed!
[2023-06-29 22:11:43,644] [INFO] Total running time: 0h0m52s