[2023-06-30 11:36:12,074] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:36:12,076] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:36:12,076] [INFO] DQC Reference Directory: /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference
[2023-06-30 11:36:13,264] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:36:13,265] [INFO] Task started: Prodigal
[2023-06-30 11:36:13,265] [INFO] Running command: gunzip -c /var/lib/cwl/stg192ee947-371f-491c-a7c1-c4f492a53ab6/GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna.gz | prodigal -d GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/cds.fna -a GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:36:20,782] [INFO] Task succeeded: Prodigal
[2023-06-30 11:36:20,782] [INFO] Task started: HMMsearch
[2023-06-30 11:36:20,782] [INFO] Running command: hmmsearch --tblout GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/reference_markers.hmm GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:36:20,912] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:36:20,913] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg192ee947-371f-491c-a7c1-c4f492a53ab6/GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna.gz]
[2023-06-30 11:36:20,933] [INFO] Query marker FASTA was written to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/markers.fasta
[2023-06-30 11:36:20,934] [INFO] Task started: Blastn
[2023-06-30 11:36:20,934] [INFO] Running command: blastn -query GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/markers.fasta -db /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/reference_markers.fasta -out GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:21,403] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:21,407] [INFO] Selected 10 target genomes.
[2023-06-30 11:36:21,407] [INFO] Target genome list was writen to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/target_genomes.txt
[2023-06-30 11:36:21,409] [INFO] Task started: fastANI
[2023-06-30 11:36:21,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg192ee947-371f-491c-a7c1-c4f492a53ab6/GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna.gz --refList GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/target_genomes.txt --output GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:36:25,930] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:25,930] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:36:25,930] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:36:25,935] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 11:36:25,935] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 11:36:25,935] [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	85.1981	175	204	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.6603	80	204	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:36:25,937] [INFO] DFAST Taxonomy check result was written to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/tc_result.tsv
[2023-06-30 11:36:25,938] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:36:25,938] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:36:25,938] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/checkm_data
[2023-06-30 11:36:25,939] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:36:25,963] [INFO] Task started: CheckM
[2023-06-30 11:36:25,963] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/checkm_input GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/checkm_result
[2023-06-30 11:36:53,830] [INFO] Task succeeded: CheckM
[2023-06-30 11:36:53,831] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 43.68%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 11:36:53,847] [INFO] ===== Completeness check finished =====
[2023-06-30 11:36:53,848] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:36:53,848] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/markers.fasta)
[2023-06-30 11:36:53,848] [INFO] Task started: Blastn
[2023-06-30 11:36:53,848] [INFO] Running command: blastn -query GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/markers.fasta -db /var/lib/cwl/stge093d150-3f46-44cd-a175-950e3bbe6761/dqc_reference/reference_markers_gtdb.fasta -out GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:36:54,303] [INFO] Task succeeded: Blastn
[2023-06-30 11:36:54,307] [INFO] Selected 9 target genomes.
[2023-06-30 11:36:54,307] [INFO] Target genome list was writen to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:36:54,308] [INFO] Task started: fastANI
[2023-06-30 11:36:54,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg192ee947-371f-491c-a7c1-c4f492a53ab6/GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna.gz --refList GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/target_genomes_gtdb.txt --output GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:36:58,108] [INFO] Task succeeded: fastANI
[2023-06-30 11:36:58,116] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 11:36:58,117] [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_000020645.1	s__Chlorobium phaeoclathratiforme	85.1981	175	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.98	1.00	1.00	2	-
GCA_903822595.1	s__Chlorobium sp903822595	83.2642	163	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903882665.1	s__Chlorobium sp903882665	82.6373	158	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	-
GCA_903939765.1	s__Chlorobium sp903939765	82.3899	152	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.90	99.86	0.94	0.94	3	-
GCA_903840935.1	s__Chlorobium sp903840935	82.1995	124	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.22	98.87	0.67	0.63	5	-
GCA_903942355.1	s__Chlorobium sp903942355	81.9531	108	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.73	99.73	0.79	0.79	2	-
GCA_903824295.1	s__Chlorobium sp903824295	81.6275	153	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_903871235.1	s__Chlorobium sp903871235	81.4646	144	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.74	99.66	0.91	0.89	5	-
GCA_903851535.1	s__Chlorobium sp903851535	80.9801	110	204	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.27	98.97	0.76	0.73	4	-
--------------------------------------------------------------------------------
[2023-06-30 11:36:58,119] [INFO] GTDB search result was written to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/result_gtdb.tsv
[2023-06-30 11:36:58,119] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:36:58,141] [INFO] DFAST_QC result json was written to GCA_903830225.1_freshwater_MAG_---_I2_bin-028_genomic.fna/dqc_result.json
[2023-06-30 11:36:58,141] [INFO] DFAST_QC completed!
[2023-06-30 11:36:58,141] [INFO] Total running time: 0h0m46s