[2023-06-13 12:27:57,466] [INFO] DFAST_QC pipeline started.
[2023-06-13 12:27:57,468] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 12:27:57,468] [INFO] DQC Reference Directory: /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference
[2023-06-13 12:27:58,867] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 12:27:58,868] [INFO] Task started: Prodigal
[2023-06-13 12:27:58,869] [INFO] Running command: gunzip -c /var/lib/cwl/stgb7d38c07-d837-42b1-867a-31cc868f64ed/GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 12:28:00,482] [INFO] Task succeeded: Prodigal
[2023-06-13 12:28:00,482] [INFO] Task started: HMMsearch
[2023-06-13 12:28:00,483] [INFO] Running command: hmmsearch --tblout GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/reference_markers.hmm GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 12:28:00,696] [INFO] Task succeeded: HMMsearch
[2023-06-13 12:28:00,697] [INFO] Found 6/6 markers.
[2023-06-13 12:28:00,710] [INFO] Query marker FASTA was written to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 12:28:00,711] [INFO] Task started: Blastn
[2023-06-13 12:28:00,711] [INFO] Running command: blastn -query GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/reference_markers.fasta -out GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:01,301] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:01,306] [INFO] Selected 15 target genomes.
[2023-06-13 12:28:01,306] [INFO] Target genome list was writen to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 12:28:01,311] [INFO] Task started: fastANI
[2023-06-13 12:28:01,312] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d38c07-d837-42b1-867a-31cc868f64ed/GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 12:28:09,062] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:09,063] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 12:28:09,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 12:28:09,065] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 12:28:09,065] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 12:28:09,065] [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
--------------------------------------------------------------------------------
[2023-06-13 12:28:09,067] [INFO] DFAST Taxonomy check result was written to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 12:28:09,067] [INFO] ===== Taxonomy check completed =====
[2023-06-13 12:28:09,068] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 12:28:09,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/checkm_data
[2023-06-13 12:28:09,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 12:28:09,083] [INFO] Task started: CheckM
[2023-06-13 12:28:09,083] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 12:28:22,579] [INFO] Task succeeded: CheckM
[2023-06-13 12:28:22,580] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.42%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2023-06-13 12:28:22,612] [INFO] ===== Completeness check finished =====
[2023-06-13 12:28:22,612] [INFO] ===== Start GTDB Search =====
[2023-06-13 12:28:22,613] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 12:28:22,613] [INFO] Task started: Blastn
[2023-06-13 12:28:22,613] [INFO] Running command: blastn -query GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg7aedde54-19c1-4b0d-9270-30fad6c17a9e/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 12:28:23,462] [INFO] Task succeeded: Blastn
[2023-06-13 12:28:23,468] [INFO] Selected 11 target genomes.
[2023-06-13 12:28:23,468] [INFO] Target genome list was writen to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 12:28:23,470] [INFO] Task started: fastANI
[2023-06-13 12:28:23,470] [INFO] Running command: fastANI --query /var/lib/cwl/stgb7d38c07-d837-42b1-867a-31cc868f64ed/GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 12:28:25,048] [INFO] Task succeeded: fastANI
[2023-06-13 12:28:25,059] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 12:28:25,060] [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
GCA_900555265.1	s__Nanosynbacter sp900555265	94.3513	143	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555425.1	s__Nanosynbacter sp900555425	94.1819	130	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555885.1	s__Nanosynbacter sp900555885	93.8624	110	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900555675.1	s__Nanosynbacter sp900555675	93.7411	128	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900556885.1	s__Nanosynbacter sp900556885	93.6463	129	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905370345.1	s__Nanosynbacter sp905370345	93.4672	139	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	97.83	97.83	0.96	0.96	2	-
GCA_900556355.1	s__Nanosynbacter sp900556355	93.2138	71	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015257705.1	s__Nanosynbacter sp015257705	92.9808	125	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007845355.1	s__Nanosynbacter sp007845355	92.9419	124	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	98.63	95.76	0.86	0.79	5	-
GCA_900557595.1	s__Nanosynbacter sp900557595	92.7494	92	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	99.88	99.88	0.97	0.97	2	-
GCA_015257635.1	s__Nanosynbacter sp015257635	92.1782	92	180	d__Bacteria;p__Patescibacteria;c__Saccharimonadia;o__Saccharimonadales;f__Nanosynbacteraceae;g__Nanosynbacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 12:28:25,062] [INFO] GTDB search result was written to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 12:28:25,063] [INFO] ===== GTDB Search completed =====
[2023-06-13 12:28:25,067] [INFO] DFAST_QC result json was written to GCA_938041365.1_ERR589525_bin.39_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 12:28:25,067] [INFO] DFAST_QC completed!
[2023-06-13 12:28:25,068] [INFO] Total running time: 0h0m28s