[2023-03-17 02:18:54,390] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:18:54,390] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:18:54,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference
[2023-03-17 02:18:56,732] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:18:56,733] [INFO] Task started: Prodigal
[2023-03-17 02:18:56,733] [INFO] Running command: cat /var/lib/cwl/stg64e4e6a1-2ac3-4876-a62f-9f689e02a892/OceanDNA-b22858.fa | prodigal -d OceanDNA-b22858/cds.fna -a OceanDNA-b22858/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:19:31,446] [INFO] Task succeeded: Prodigal
[2023-03-17 02:19:31,447] [INFO] Task started: HMMsearch
[2023-03-17 02:19:31,447] [INFO] Running command: hmmsearch --tblout OceanDNA-b22858/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/reference_markers.hmm OceanDNA-b22858/protein.faa > /dev/null
[2023-03-17 02:19:31,683] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:19:31,684] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg64e4e6a1-2ac3-4876-a62f-9f689e02a892/OceanDNA-b22858.fa]
[2023-03-17 02:19:31,715] [INFO] Query marker FASTA was written to OceanDNA-b22858/markers.fasta
[2023-03-17 02:19:31,716] [INFO] Task started: Blastn
[2023-03-17 02:19:31,716] [INFO] Running command: blastn -query OceanDNA-b22858/markers.fasta -db /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/reference_markers.fasta -out OceanDNA-b22858/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:19:32,228] [INFO] Task succeeded: Blastn
[2023-03-17 02:19:32,229] [INFO] Selected 22 target genomes.
[2023-03-17 02:19:32,229] [INFO] Target genome list was writen to OceanDNA-b22858/target_genomes.txt
[2023-03-17 02:19:32,241] [INFO] Task started: fastANI
[2023-03-17 02:19:32,241] [INFO] Running command: fastANI --query /var/lib/cwl/stg64e4e6a1-2ac3-4876-a62f-9f689e02a892/OceanDNA-b22858.fa --refList OceanDNA-b22858/target_genomes.txt --output OceanDNA-b22858/fastani_result.tsv --threads 1
[2023-03-17 02:19:52,378] [INFO] Task succeeded: fastANI
[2023-03-17 02:19:52,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:19:52,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:19:52,379] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 02:19:52,379] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 02:19:52,379] [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
--------------------------------------------------------------------------------
[2023-03-17 02:19:52,379] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22858/tc_result.tsv
[2023-03-17 02:19:52,379] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:19:52,380] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:19:52,380] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/checkm_data
[2023-03-17 02:19:52,384] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:19:52,392] [INFO] Task started: CheckM
[2023-03-17 02:19:52,392] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22858/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22858/checkm_input OceanDNA-b22858/checkm_result
[2023-03-17 02:21:18,985] [INFO] Task succeeded: CheckM
[2023-03-17 02:21:18,986] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:21:18,989] [INFO] ===== Completeness check finished =====
[2023-03-17 02:21:18,989] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:21:18,990] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22858/markers.fasta)
[2023-03-17 02:21:18,991] [INFO] Task started: Blastn
[2023-03-17 02:21:18,991] [INFO] Running command: blastn -query OceanDNA-b22858/markers.fasta -db /var/lib/cwl/stg4e11a4d8-59b6-4dc7-a6e7-0897263a6d16/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22858/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:21:19,742] [INFO] Task succeeded: Blastn
[2023-03-17 02:21:19,744] [INFO] Selected 17 target genomes.
[2023-03-17 02:21:19,744] [INFO] Target genome list was writen to OceanDNA-b22858/target_genomes_gtdb.txt
[2023-03-17 02:21:20,432] [INFO] Task started: fastANI
[2023-03-17 02:21:20,432] [INFO] Running command: fastANI --query /var/lib/cwl/stg64e4e6a1-2ac3-4876-a62f-9f689e02a892/OceanDNA-b22858.fa --refList OceanDNA-b22858/target_genomes_gtdb.txt --output OceanDNA-b22858/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:21:35,462] [INFO] Task succeeded: fastANI
[2023-03-17 02:21:35,468] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:21:35,468] [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_017859815.1	s__SXXK01 sp017859815	96.6029	1454	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903924405.1	s__SXXK01 sp903924405	75.9032	98	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.71	99.71	0.88	0.88	2	-
GCA_005791255.1	s__SXXK01 sp005791255	75.8071	102	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	98.10	98.10	0.89	0.89	2	-
GCA_016795145.1	s__SXXK01 sp016795145	75.7891	80	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871805.1	s__SXXK01 sp903871805	75.6756	90	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.56	99.46	0.84	0.84	3	-
GCA_903896675.1	s__SXXK01 sp903896675	75.675	118	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.51	99.43	0.86	0.84	7	-
GCA_903858815.1	s__SXXK01 sp903858815	75.448	134	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__SXXK01	95.0	99.79	99.79	0.88	0.88	2	-
GCA_014238335.1	s__Fuerstia sp014238335	75.1894	61	1838	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Planctomycetales;f__Planctomycetaceae;g__Fuerstia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:21:35,470] [INFO] GTDB search result was written to OceanDNA-b22858/result_gtdb.tsv
[2023-03-17 02:21:35,471] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:21:35,473] [INFO] DFAST_QC result json was written to OceanDNA-b22858/dqc_result.json
[2023-03-17 02:21:35,474] [INFO] DFAST_QC completed!
[2023-03-17 02:21:35,474] [INFO] Total running time: 0h2m41s