[2023-06-08 09:54:30,858] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:54:30,860] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:54:30,860] [INFO] DQC Reference Directory: /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference
[2023-06-08 09:54:32,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:54:32,944] [INFO] Task started: Prodigal
[2023-06-08 09:54:32,945] [INFO] Running command: gunzip -c /var/lib/cwl/stge1c13667-31dd-4c0f-805d-4ca83b18ec7b/GCA_945898005.1_MsH-30jul19-126_genomic.fna.gz | prodigal -d GCA_945898005.1_MsH-30jul19-126_genomic.fna/cds.fna -a GCA_945898005.1_MsH-30jul19-126_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:54:43,442] [INFO] Task succeeded: Prodigal
[2023-06-08 09:54:43,443] [INFO] Task started: HMMsearch
[2023-06-08 09:54:43,443] [INFO] Running command: hmmsearch --tblout GCA_945898005.1_MsH-30jul19-126_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/reference_markers.hmm GCA_945898005.1_MsH-30jul19-126_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:54:43,681] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:54:43,682] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge1c13667-31dd-4c0f-805d-4ca83b18ec7b/GCA_945898005.1_MsH-30jul19-126_genomic.fna.gz]
[2023-06-08 09:54:43,713] [INFO] Query marker FASTA was written to GCA_945898005.1_MsH-30jul19-126_genomic.fna/markers.fasta
[2023-06-08 09:54:43,714] [INFO] Task started: Blastn
[2023-06-08 09:54:43,714] [INFO] Running command: blastn -query GCA_945898005.1_MsH-30jul19-126_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/reference_markers.fasta -out GCA_945898005.1_MsH-30jul19-126_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:54:44,209] [INFO] Task succeeded: Blastn
[2023-06-08 09:54:44,214] [INFO] Selected 12 target genomes.
[2023-06-08 09:54:44,214] [INFO] Target genome list was writen to GCA_945898005.1_MsH-30jul19-126_genomic.fna/target_genomes.txt
[2023-06-08 09:54:44,217] [INFO] Task started: fastANI
[2023-06-08 09:54:44,217] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c13667-31dd-4c0f-805d-4ca83b18ec7b/GCA_945898005.1_MsH-30jul19-126_genomic.fna.gz --refList GCA_945898005.1_MsH-30jul19-126_genomic.fna/target_genomes.txt --output GCA_945898005.1_MsH-30jul19-126_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:54:51,327] [INFO] Task succeeded: fastANI
[2023-06-08 09:54:51,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:54:51,328] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:54:51,330] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:54:51,331] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:54:51,331] [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
--------------------------------------------------------------------------------
[2023-06-08 09:54:51,333] [INFO] DFAST Taxonomy check result was written to GCA_945898005.1_MsH-30jul19-126_genomic.fna/tc_result.tsv
[2023-06-08 09:54:51,334] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:54:51,334] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:54:51,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/checkm_data
[2023-06-08 09:54:51,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:54:51,372] [INFO] Task started: CheckM
[2023-06-08 09:54:51,373] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945898005.1_MsH-30jul19-126_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945898005.1_MsH-30jul19-126_genomic.fna/checkm_input GCA_945898005.1_MsH-30jul19-126_genomic.fna/checkm_result
[2023-06-08 09:55:26,815] [INFO] Task succeeded: CheckM
[2023-06-08 09:55:26,816] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:55:26,846] [INFO] ===== Completeness check finished =====
[2023-06-08 09:55:26,846] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:55:26,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945898005.1_MsH-30jul19-126_genomic.fna/markers.fasta)
[2023-06-08 09:55:26,847] [INFO] Task started: Blastn
[2023-06-08 09:55:26,847] [INFO] Running command: blastn -query GCA_945898005.1_MsH-30jul19-126_genomic.fna/markers.fasta -db /var/lib/cwl/stg7d5fb315-2ebe-4deb-bc10-86352e107550/dqc_reference/reference_markers_gtdb.fasta -out GCA_945898005.1_MsH-30jul19-126_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:55:27,343] [INFO] Task succeeded: Blastn
[2023-06-08 09:55:27,348] [INFO] Selected 12 target genomes.
[2023-06-08 09:55:27,348] [INFO] Target genome list was writen to GCA_945898005.1_MsH-30jul19-126_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:55:27,353] [INFO] Task started: fastANI
[2023-06-08 09:55:27,353] [INFO] Running command: fastANI --query /var/lib/cwl/stge1c13667-31dd-4c0f-805d-4ca83b18ec7b/GCA_945898005.1_MsH-30jul19-126_genomic.fna.gz --refList GCA_945898005.1_MsH-30jul19-126_genomic.fna/target_genomes_gtdb.txt --output GCA_945898005.1_MsH-30jul19-126_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:55:32,950] [INFO] Task succeeded: fastANI
[2023-06-08 09:55:32,961] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:55:32,961] [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_002737585.1	s__UBA966 sp002737585	96.113	354	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	99.34	99.34	0.70	0.70	2	conclusive
GCA_002292895.1	s__UBA966 sp002292895	92.1542	626	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	99.22	99.02	0.83	0.82	3	-
GCA_018883105.1	s__UBA966 sp018883105	77.3257	139	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873255.1	s__UBA966 sp016873255	77.2523	223	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA966	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872835.1	s__SYAC01 sp016872835	76.7287	63	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903867275.1	s__SYAC01 sp903867275	76.6109	56	947	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SYAC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:55:32,963] [INFO] GTDB search result was written to GCA_945898005.1_MsH-30jul19-126_genomic.fna/result_gtdb.tsv
[2023-06-08 09:55:32,963] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:55:32,966] [INFO] DFAST_QC result json was written to GCA_945898005.1_MsH-30jul19-126_genomic.fna/dqc_result.json
[2023-06-08 09:55:32,966] [INFO] DFAST_QC completed!
[2023-06-08 09:55:32,966] [INFO] Total running time: 0h1m2s