[2023-06-13 18:25:31,711] [INFO] DFAST_QC pipeline started.
[2023-06-13 18:25:31,720] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 18:25:31,720] [INFO] DQC Reference Directory: /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference
[2023-06-13 18:25:32,797] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 18:25:32,798] [INFO] Task started: Prodigal
[2023-06-13 18:25:32,798] [INFO] Running command: gunzip -c /var/lib/cwl/stg806e2cfe-ec2f-4b3c-b088-691be44b7c39/GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 18:25:37,874] [INFO] Task succeeded: Prodigal
[2023-06-13 18:25:37,875] [INFO] Task started: HMMsearch
[2023-06-13 18:25:37,875] [INFO] Running command: hmmsearch --tblout GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/reference_markers.hmm GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-13 18:25:38,069] [INFO] Task succeeded: HMMsearch
[2023-06-13 18:25:38,070] [INFO] Found 6/6 markers.
[2023-06-13 18:25:38,098] [INFO] Query marker FASTA was written to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-13 18:25:38,099] [INFO] Task started: Blastn
[2023-06-13 18:25:38,099] [INFO] Running command: blastn -query GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/reference_markers.fasta -out GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:25:38,613] [INFO] Task succeeded: Blastn
[2023-06-13 18:25:38,619] [INFO] Selected 29 target genomes.
[2023-06-13 18:25:38,620] [INFO] Target genome list was writen to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-13 18:25:38,623] [INFO] Task started: fastANI
[2023-06-13 18:25:38,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg806e2cfe-ec2f-4b3c-b088-691be44b7c39/GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 18:25:56,284] [INFO] Task succeeded: fastANI
[2023-06-13 18:25:56,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 18:25:56,285] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 18:25:56,287] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 18:25:56,287] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 18:25:56,287] [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 18:25:56,289] [INFO] DFAST Taxonomy check result was written to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-13 18:25:56,290] [INFO] ===== Taxonomy check completed =====
[2023-06-13 18:25:56,290] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 18:25:56,290] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/checkm_data
[2023-06-13 18:25:56,293] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 18:25:56,323] [INFO] Task started: CheckM
[2023-06-13 18:25:56,324] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-13 18:26:17,206] [INFO] Task succeeded: CheckM
[2023-06-13 18:26:17,207] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.32%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 18:26:17,227] [INFO] ===== Completeness check finished =====
[2023-06-13 18:26:17,227] [INFO] ===== Start GTDB Search =====
[2023-06-13 18:26:17,229] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-13 18:26:17,229] [INFO] Task started: Blastn
[2023-06-13 18:26:17,229] [INFO] Running command: blastn -query GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg990a9a3f-38fc-40d4-b939-25bbefa2e16d/dqc_reference/reference_markers_gtdb.fasta -out GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 18:26:17,996] [INFO] Task succeeded: Blastn
[2023-06-13 18:26:18,000] [INFO] Selected 25 target genomes.
[2023-06-13 18:26:18,000] [INFO] Target genome list was writen to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 18:26:18,006] [INFO] Task started: fastANI
[2023-06-13 18:26:18,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg806e2cfe-ec2f-4b3c-b088-691be44b7c39/GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 18:26:29,809] [INFO] Task succeeded: fastANI
[2023-06-13 18:26:29,813] [INFO] Found 4 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 18:26:29,813] [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_018713435.1	s__Merdiplasma excrementigallinarum	80.1938	153	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905207905.1	s__Merdiplasma sp905207905	78.3131	55	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900770325.1	s__Merdiplasma sp900770325	77.4765	67	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Merdiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018713585.1	s__Pullilachnospira stercoravium	76.7724	50	349	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Pullilachnospira	95.0	97.91	97.84	0.85	0.79	6	-
--------------------------------------------------------------------------------
[2023-06-13 18:26:29,814] [INFO] GTDB search result was written to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-13 18:26:29,815] [INFO] ===== GTDB Search completed =====
[2023-06-13 18:26:29,816] [INFO] DFAST_QC result json was written to GCA_938014505.1_ERR732777_bin.40_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-13 18:26:29,817] [INFO] DFAST_QC completed!
[2023-06-13 18:26:29,817] [INFO] Total running time: 0h0m58s