[2023-06-30 12:34:07,157] [INFO] DFAST_QC pipeline started.
[2023-06-30 12:34:07,164] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 12:34:07,164] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference
[2023-06-30 12:34:09,808] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 12:34:09,809] [INFO] Task started: Prodigal
[2023-06-30 12:34:09,809] [INFO] Running command: gunzip -c /var/lib/cwl/stg18c8b343-3f68-4fd8-8ba0-71d7aa5f0ce4/GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna.gz | prodigal -d GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/cds.fna -a GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 12:34:21,022] [INFO] Task succeeded: Prodigal
[2023-06-30 12:34:21,023] [INFO] Task started: HMMsearch
[2023-06-30 12:34:21,023] [INFO] Running command: hmmsearch --tblout GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/reference_markers.hmm GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/protein.faa > /dev/null
[2023-06-30 12:34:21,324] [INFO] Task succeeded: HMMsearch
[2023-06-30 12:34:21,325] [INFO] Found 6/6 markers.
[2023-06-30 12:34:21,368] [INFO] Query marker FASTA was written to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/markers.fasta
[2023-06-30 12:34:21,368] [INFO] Task started: Blastn
[2023-06-30 12:34:21,368] [INFO] Running command: blastn -query GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/reference_markers.fasta -out GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:34:21,960] [INFO] Task succeeded: Blastn
[2023-06-30 12:34:21,965] [INFO] Selected 17 target genomes.
[2023-06-30 12:34:21,966] [INFO] Target genome list was writen to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/target_genomes.txt
[2023-06-30 12:34:21,969] [INFO] Task started: fastANI
[2023-06-30 12:34:21,969] [INFO] Running command: fastANI --query /var/lib/cwl/stg18c8b343-3f68-4fd8-8ba0-71d7aa5f0ce4/GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna.gz --refList GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/target_genomes.txt --output GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 12:34:34,979] [INFO] Task succeeded: fastANI
[2023-06-30 12:34:34,980] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 12:34:34,980] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 12:34:34,987] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 12:34:34,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 12:34:34,988] [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
Oscillochloris trichoides	strain=DG-6	GCA_000152145.1	104176	104176	type	True	77.7005	312	1230	95	below_threshold
Chloroflexus islandicus	strain=isl-2	GCA_001650695.1	1707952	1707952	type	True	76.0065	98	1230	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	74.7265	54	1230	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 12:34:34,990] [INFO] DFAST Taxonomy check result was written to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/tc_result.tsv
[2023-06-30 12:34:34,991] [INFO] ===== Taxonomy check completed =====
[2023-06-30 12:34:34,991] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 12:34:34,992] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/checkm_data
[2023-06-30 12:34:34,994] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 12:34:35,044] [INFO] Task started: CheckM
[2023-06-30 12:34:35,044] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/checkm_input GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/checkm_result
[2023-06-30 12:35:12,259] [INFO] Task succeeded: CheckM
[2023-06-30 12:35:12,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 12:35:12,283] [INFO] ===== Completeness check finished =====
[2023-06-30 12:35:12,284] [INFO] ===== Start GTDB Search =====
[2023-06-30 12:35:12,284] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/markers.fasta)
[2023-06-30 12:35:12,285] [INFO] Task started: Blastn
[2023-06-30 12:35:12,285] [INFO] Running command: blastn -query GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/markers.fasta -db /var/lib/cwl/stgcd284d77-cb18-41ab-9181-39d060f87141/dqc_reference/reference_markers_gtdb.fasta -out GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 12:35:13,070] [INFO] Task succeeded: Blastn
[2023-06-30 12:35:13,078] [INFO] Selected 11 target genomes.
[2023-06-30 12:35:13,078] [INFO] Target genome list was writen to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 12:35:13,084] [INFO] Task started: fastANI
[2023-06-30 12:35:13,084] [INFO] Running command: fastANI --query /var/lib/cwl/stg18c8b343-3f68-4fd8-8ba0-71d7aa5f0ce4/GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna.gz --refList GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/target_genomes_gtdb.txt --output GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 12:35:28,950] [INFO] Task succeeded: fastANI
[2023-06-30 12:35:28,966] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 12:35:28,966] [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_903877945.1	s__Oscillochloris sp903877945	99.4036	967	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.99	98.27	0.81	0.73	10	conclusive
GCA_903920315.1	s__Oscillochloris sp903920315	83.5027	796	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	98.25	98.25	0.71	0.71	2	-
GCA_903887465.1	s__Oscillochloris sp903887465	83.3296	754	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	99.82	99.74	0.95	0.93	6	-
GCA_004138175.2	s__Oscillochloris sp004138175	80.6741	748	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916565.1	s__CAIWXH01 sp903916565	79.7481	323	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__CAIWXH01	95.0	98.56	98.56	0.77	0.77	2	-
GCF_000152145.1	s__Oscillochloris trichoides	77.6906	313	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004138135.1	s__Oscillochloris fontis	77.6676	295	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__Oscillochloris	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388805.1	s__JACAEO01 sp013388805	77.292	267	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__JACAEO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004367505.1	s__OHK40 sp004367505	76.7179	289	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Chloroflexaceae;g__OHK40	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013538855.1	s__OHK22 sp013538855	75.1722	78	1230	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Herpetosiphonaceae;g__OHK22	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 12:35:28,969] [INFO] GTDB search result was written to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/result_gtdb.tsv
[2023-06-30 12:35:28,969] [INFO] ===== GTDB Search completed =====
[2023-06-30 12:35:28,973] [INFO] DFAST_QC result json was written to GCA_903898955.1_freshwater_MAG_---_LJ_bin-0871_genomic.fna/dqc_result.json
[2023-06-30 12:35:28,973] [INFO] DFAST_QC completed!
[2023-06-30 12:35:28,973] [INFO] Total running time: 0h1m22s