[2023-06-05 18:24:58,426] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:24:58,428] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:24:58,428] [INFO] DQC Reference Directory: /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference
[2023-06-05 18:24:59,521] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:24:59,522] [INFO] Task started: Prodigal
[2023-06-05 18:24:59,522] [INFO] Running command: gunzip -c /var/lib/cwl/stgab10d291-03c0-476f-acbd-61fbab5ead97/GCA_934474795.1_ERR7738621_bin.187_genomic.fna.gz | prodigal -d GCA_934474795.1_ERR7738621_bin.187_genomic.fna/cds.fna -a GCA_934474795.1_ERR7738621_bin.187_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:25:05,271] [INFO] Task succeeded: Prodigal
[2023-06-05 18:25:05,271] [INFO] Task started: HMMsearch
[2023-06-05 18:25:05,272] [INFO] Running command: hmmsearch --tblout GCA_934474795.1_ERR7738621_bin.187_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/reference_markers.hmm GCA_934474795.1_ERR7738621_bin.187_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:25:05,474] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:25:05,475] [INFO] Found 6/6 markers.
[2023-06-05 18:25:05,498] [INFO] Query marker FASTA was written to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/markers.fasta
[2023-06-05 18:25:05,498] [INFO] Task started: Blastn
[2023-06-05 18:25:05,498] [INFO] Running command: blastn -query GCA_934474795.1_ERR7738621_bin.187_genomic.fna/markers.fasta -db /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/reference_markers.fasta -out GCA_934474795.1_ERR7738621_bin.187_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:25:06,152] [INFO] Task succeeded: Blastn
[2023-06-05 18:25:06,156] [INFO] Selected 20 target genomes.
[2023-06-05 18:25:06,156] [INFO] Target genome list was writen to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/target_genomes.txt
[2023-06-05 18:25:06,164] [INFO] Task started: fastANI
[2023-06-05 18:25:06,165] [INFO] Running command: fastANI --query /var/lib/cwl/stgab10d291-03c0-476f-acbd-61fbab5ead97/GCA_934474795.1_ERR7738621_bin.187_genomic.fna.gz --refList GCA_934474795.1_ERR7738621_bin.187_genomic.fna/target_genomes.txt --output GCA_934474795.1_ERR7738621_bin.187_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:25:18,646] [INFO] Task succeeded: fastANI
[2023-06-05 18:25:18,646] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:25:18,647] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:25:18,648] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:25:18,648] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:25:18,648] [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
--------------------------------------------------------------------------------
[2023-06-05 18:25:18,650] [INFO] DFAST Taxonomy check result was written to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/tc_result.tsv
[2023-06-05 18:25:18,650] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:25:18,650] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:25:18,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/checkm_data
[2023-06-05 18:25:18,653] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:25:18,681] [INFO] Task started: CheckM
[2023-06-05 18:25:18,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934474795.1_ERR7738621_bin.187_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934474795.1_ERR7738621_bin.187_genomic.fna/checkm_input GCA_934474795.1_ERR7738621_bin.187_genomic.fna/checkm_result
[2023-06-05 18:25:40,668] [INFO] Task succeeded: CheckM
[2023-06-05 18:25:40,669] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:25:40,686] [INFO] ===== Completeness check finished =====
[2023-06-05 18:25:40,686] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:25:40,686] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934474795.1_ERR7738621_bin.187_genomic.fna/markers.fasta)
[2023-06-05 18:25:40,687] [INFO] Task started: Blastn
[2023-06-05 18:25:40,687] [INFO] Running command: blastn -query GCA_934474795.1_ERR7738621_bin.187_genomic.fna/markers.fasta -db /var/lib/cwl/stgb001508e-37a2-46ab-9b53-ad16a2da83ae/dqc_reference/reference_markers_gtdb.fasta -out GCA_934474795.1_ERR7738621_bin.187_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:25:41,675] [INFO] Task succeeded: Blastn
[2023-06-05 18:25:41,679] [INFO] Selected 27 target genomes.
[2023-06-05 18:25:41,679] [INFO] Target genome list was writen to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:25:41,739] [INFO] Task started: fastANI
[2023-06-05 18:25:41,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgab10d291-03c0-476f-acbd-61fbab5ead97/GCA_934474795.1_ERR7738621_bin.187_genomic.fna.gz --refList GCA_934474795.1_ERR7738621_bin.187_genomic.fna/target_genomes_gtdb.txt --output GCA_934474795.1_ERR7738621_bin.187_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:25:55,916] [INFO] Task succeeded: fastANI
[2023-06-05 18:25:55,923] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:25:55,923] [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_015069015.1	s__RGIG1828 sp015069015	77.5681	70	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016293435.1	s__RGIG1828 sp016293435	77.5487	79	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017397885.1	s__RGIG1828 sp017397885	77.4247	78	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017437345.1	s__RGIG1828 sp017437345	77.2214	53	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015068985.1	s__RGIG1828 sp015068985	77.1028	73	890	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__UMGS1810;f__UMGS1810;g__RGIG1828	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:25:55,926] [INFO] GTDB search result was written to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/result_gtdb.tsv
[2023-06-05 18:25:55,927] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:25:55,930] [INFO] DFAST_QC result json was written to GCA_934474795.1_ERR7738621_bin.187_genomic.fna/dqc_result.json
[2023-06-05 18:25:55,930] [INFO] DFAST_QC completed!
[2023-06-05 18:25:55,930] [INFO] Total running time: 0h0m58s