[2023-06-18 23:43:17,806] [INFO] DFAST_QC pipeline started.
[2023-06-18 23:43:17,808] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 23:43:17,809] [INFO] DQC Reference Directory: /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference
[2023-06-18 23:43:19,236] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 23:43:19,240] [INFO] Task started: Prodigal
[2023-06-18 23:43:19,240] [INFO] Running command: gunzip -c /var/lib/cwl/stg9f7b2d38-171d-4313-8036-4692438ee362/GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 23:43:25,093] [INFO] Task succeeded: Prodigal
[2023-06-18 23:43:25,093] [INFO] Task started: HMMsearch
[2023-06-18 23:43:25,093] [INFO] Running command: hmmsearch --tblout GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/reference_markers.hmm GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-18 23:43:25,368] [INFO] Task succeeded: HMMsearch
[2023-06-18 23:43:25,369] [INFO] Found 6/6 markers.
[2023-06-18 23:43:25,402] [INFO] Query marker FASTA was written to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-18 23:43:25,402] [INFO] Task started: Blastn
[2023-06-18 23:43:25,403] [INFO] Running command: blastn -query GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/reference_markers.fasta -out GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:43:26,167] [INFO] Task succeeded: Blastn
[2023-06-18 23:43:26,171] [INFO] Selected 23 target genomes.
[2023-06-18 23:43:26,171] [INFO] Target genome list was writen to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-18 23:43:26,204] [INFO] Task started: fastANI
[2023-06-18 23:43:26,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7b2d38-171d-4313-8036-4692438ee362/GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 23:43:42,399] [INFO] Task succeeded: fastANI
[2023-06-18 23:43:42,400] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 23:43:42,400] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 23:43:42,402] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 23:43:42,402] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-18 23:43:42,402] [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
--------------------------------------------------------------------------------
[2023-06-18 23:43:42,404] [INFO] DFAST Taxonomy check result was written to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-18 23:43:42,404] [INFO] ===== Taxonomy check completed =====
[2023-06-18 23:43:42,405] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 23:43:42,405] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/checkm_data
[2023-06-18 23:43:42,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 23:43:42,433] [INFO] Task started: CheckM
[2023-06-18 23:43:42,433] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-18 23:44:06,731] [INFO] Task succeeded: CheckM
[2023-06-18 23:44:06,733] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 23:44:06,753] [INFO] ===== Completeness check finished =====
[2023-06-18 23:44:06,754] [INFO] ===== Start GTDB Search =====
[2023-06-18 23:44:06,754] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-18 23:44:06,755] [INFO] Task started: Blastn
[2023-06-18 23:44:06,755] [INFO] Running command: blastn -query GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg8d554e16-650d-44ea-9eb9-249b8e97f63d/dqc_reference/reference_markers_gtdb.fasta -out GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 23:44:07,822] [INFO] Task succeeded: Blastn
[2023-06-18 23:44:07,828] [INFO] Selected 27 target genomes.
[2023-06-18 23:44:07,828] [INFO] Target genome list was writen to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 23:44:07,949] [INFO] Task started: fastANI
[2023-06-18 23:44:07,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg9f7b2d38-171d-4313-8036-4692438ee362/GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 23:44:22,718] [INFO] Task succeeded: fastANI
[2023-06-18 23:44:22,726] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 23:44:22,727] [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_008087055.1	s__HIMB30 sp008087055	78.1402	80	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000227525.2	s__HIMB30 sp000227525	77.8583	88	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	98.38	98.38	0.91	0.91	2	-
GCA_009886945.1	s__HIMB30 sp002691485	77.441	82	557	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Litoricolaceae;g__HIMB30	95.0	97.88	95.73	0.81	0.62	14	-
--------------------------------------------------------------------------------
[2023-06-18 23:44:22,729] [INFO] GTDB search result was written to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-18 23:44:22,730] [INFO] ===== GTDB Search completed =====
[2023-06-18 23:44:22,732] [INFO] DFAST_QC result json was written to GCA_937930145.1_ERR1995205_bin.64_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-18 23:44:22,732] [INFO] DFAST_QC completed!
[2023-06-18 23:44:22,732] [INFO] Total running time: 0h1m5s