[2023-06-13 03:52:15,570] [INFO] DFAST_QC pipeline started.
[2023-06-13 03:52:15,572] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 03:52:15,572] [INFO] DQC Reference Directory: /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference
[2023-06-13 03:52:16,915] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 03:52:16,916] [INFO] Task started: Prodigal
[2023-06-13 03:52:16,917] [INFO] Running command: gunzip -c /var/lib/cwl/stg959f4ea2-057f-4ca3-8581-be034b970e1d/GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 03:52:30,366] [INFO] Task succeeded: Prodigal
[2023-06-13 03:52:30,367] [INFO] Task started: HMMsearch
[2023-06-13 03:52:30,367] [INFO] Running command: hmmsearch --tblout GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/reference_markers.hmm GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 03:52:30,614] [INFO] Task succeeded: HMMsearch
[2023-06-13 03:52:30,616] [INFO] Found 6/6 markers.
[2023-06-13 03:52:30,643] [INFO] Query marker FASTA was written to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 03:52:30,644] [INFO] Task started: Blastn
[2023-06-13 03:52:30,644] [INFO] Running command: blastn -query GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/reference_markers.fasta -out GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:52:31,264] [INFO] Task succeeded: Blastn
[2023-06-13 03:52:31,272] [INFO] Selected 17 target genomes.
[2023-06-13 03:52:31,273] [INFO] Target genome list was writen to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 03:52:31,299] [INFO] Task started: fastANI
[2023-06-13 03:52:31,300] [INFO] Running command: fastANI --query /var/lib/cwl/stg959f4ea2-057f-4ca3-8581-be034b970e1d/GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 03:52:42,142] [INFO] Task succeeded: fastANI
[2023-06-13 03:52:42,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 03:52:42,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 03:52:42,144] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 03:52:42,144] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 03:52:42,144] [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 03:52:42,146] [INFO] DFAST Taxonomy check result was written to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 03:52:42,147] [INFO] ===== Taxonomy check completed =====
[2023-06-13 03:52:42,147] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 03:52:42,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/checkm_data
[2023-06-13 03:52:42,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 03:52:42,180] [INFO] Task started: CheckM
[2023-06-13 03:52:42,181] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 03:53:21,217] [INFO] Task succeeded: CheckM
[2023-06-13 03:53:21,218] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 03:53:21,238] [INFO] ===== Completeness check finished =====
[2023-06-13 03:53:21,239] [INFO] ===== Start GTDB Search =====
[2023-06-13 03:53:21,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 03:53:21,239] [INFO] Task started: Blastn
[2023-06-13 03:53:21,240] [INFO] Running command: blastn -query GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg75a197fe-6adc-4ac0-a7b3-e9476a20f598/dqc_reference/reference_markers_gtdb.fasta -out GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 03:53:22,142] [INFO] Task succeeded: Blastn
[2023-06-13 03:53:22,165] [INFO] Selected 6 target genomes.
[2023-06-13 03:53:22,165] [INFO] Target genome list was writen to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 03:53:22,168] [INFO] Task started: fastANI
[2023-06-13 03:53:22,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg959f4ea2-057f-4ca3-8581-be034b970e1d/GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 03:53:25,996] [INFO] Task succeeded: fastANI
[2023-06-13 03:53:26,007] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 03:53:26,007] [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_900760665.1	s__Merdousia sp900760665	97.9558	723	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	97.95	97.87	0.94	0.93	3	conclusive
GCA_904424815.1	s__Merdousia sp001917305	92.0591	703	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.91	98.75	0.96	0.93	5	-
GCA_905214995.1	s__Merdousia sp905214995	91.1962	558	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002437405.1	s__Merdousia sp002437405	78.6931	335	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.41	95.60	0.92	0.87	4	-
GCA_900545715.1	s__Merdousia gallistercoris	78.6093	312	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.74	98.74	0.93	0.91	5	-
GCA_900545705.1	s__Merdousia sp900545705	78.0687	319	803	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__CAG-312;g__Merdousia	95.0	98.53	98.52	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2023-06-13 03:53:26,009] [INFO] GTDB search result was written to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 03:53:26,009] [INFO] ===== GTDB Search completed =====
[2023-06-13 03:53:26,030] [INFO] DFAST_QC result json was written to GCA_938042335.1_ERR1430523_bin.8_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 03:53:26,030] [INFO] DFAST_QC completed!
[2023-06-13 03:53:26,030] [INFO] Total running time: 0h1m10s