[2023-03-19 02:05:13,324] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:05:13,325] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:05:13,325] [INFO] DQC Reference Directory: /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference
[2023-03-19 02:05:14,471] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:05:14,471] [INFO] Task started: Prodigal
[2023-03-19 02:05:14,472] [INFO] Running command: cat /var/lib/cwl/stg2be2bb53-7eaf-496f-8234-0eff1f1c1c95/OceanDNA-b22193.fa | prodigal -d OceanDNA-b22193/cds.fna -a OceanDNA-b22193/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:05:21,050] [INFO] Task succeeded: Prodigal
[2023-03-19 02:05:21,050] [INFO] Task started: HMMsearch
[2023-03-19 02:05:21,051] [INFO] Running command: hmmsearch --tblout OceanDNA-b22193/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/reference_markers.hmm OceanDNA-b22193/protein.faa > /dev/null
[2023-03-19 02:05:21,224] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:05:21,224] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2be2bb53-7eaf-496f-8234-0eff1f1c1c95/OceanDNA-b22193.fa]
[2023-03-19 02:05:21,236] [INFO] Query marker FASTA was written to OceanDNA-b22193/markers.fasta
[2023-03-19 02:05:21,237] [INFO] Task started: Blastn
[2023-03-19 02:05:21,237] [INFO] Running command: blastn -query OceanDNA-b22193/markers.fasta -db /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/reference_markers.fasta -out OceanDNA-b22193/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:05:21,771] [INFO] Task succeeded: Blastn
[2023-03-19 02:05:21,772] [INFO] Selected 16 target genomes.
[2023-03-19 02:05:21,773] [INFO] Target genome list was writen to OceanDNA-b22193/target_genomes.txt
[2023-03-19 02:05:21,782] [INFO] Task started: fastANI
[2023-03-19 02:05:21,782] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be2bb53-7eaf-496f-8234-0eff1f1c1c95/OceanDNA-b22193.fa --refList OceanDNA-b22193/target_genomes.txt --output OceanDNA-b22193/fastani_result.tsv --threads 1
[2023-03-19 02:05:35,833] [INFO] Task succeeded: fastANI
[2023-03-19 02:05:35,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:05:35,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:05:35,834] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:05:35,834] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:05:35,834] [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
--------------------------------------------------------------------------------
[2023-03-19 02:05:35,834] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22193/tc_result.tsv
[2023-03-19 02:05:35,835] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:05:35,835] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:05:35,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/checkm_data
[2023-03-19 02:05:35,837] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:05:35,841] [INFO] Task started: CheckM
[2023-03-19 02:05:35,841] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22193/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22193/checkm_input OceanDNA-b22193/checkm_result
[2023-03-19 02:06:04,366] [INFO] Task succeeded: CheckM
[2023-03-19 02:06:04,366] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.32%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:06:04,368] [INFO] ===== Completeness check finished =====
[2023-03-19 02:06:04,368] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:06:04,368] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22193/markers.fasta)
[2023-03-19 02:06:04,369] [INFO] Task started: Blastn
[2023-03-19 02:06:04,369] [INFO] Running command: blastn -query OceanDNA-b22193/markers.fasta -db /var/lib/cwl/stg986bd6ff-c1b3-4762-ab0a-304fb035990d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22193/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:06:05,151] [INFO] Task succeeded: Blastn
[2023-03-19 02:06:05,152] [INFO] Selected 15 target genomes.
[2023-03-19 02:06:05,152] [INFO] Target genome list was writen to OceanDNA-b22193/target_genomes_gtdb.txt
[2023-03-19 02:06:05,441] [INFO] Task started: fastANI
[2023-03-19 02:06:05,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg2be2bb53-7eaf-496f-8234-0eff1f1c1c95/OceanDNA-b22193.fa --refList OceanDNA-b22193/target_genomes_gtdb.txt --output OceanDNA-b22193/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:06:11,960] [INFO] Task succeeded: fastANI
[2023-03-19 02:06:11,964] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 02:06:11,964] [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_002722935.1	s__SP202 sp002722935	98.2334	181	274	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_014238205.1	s__SP202 sp014238205	81.726	225	274	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__SP202	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364485.1	s__UBA854 sp002364485	77.3478	92	274	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.87	99.87	0.97	0.97	2	-
GCA_002295885.1	s__UBA854 sp002295885	77.2986	85	274	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	99.78	99.78	0.94	0.94	2	-
GCA_002591705.1	s__UBA854 sp002591705	76.6598	65	274	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA854	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 02:06:11,964] [INFO] GTDB search result was written to OceanDNA-b22193/result_gtdb.tsv
[2023-03-19 02:06:11,965] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:06:11,965] [INFO] DFAST_QC result json was written to OceanDNA-b22193/dqc_result.json
[2023-03-19 02:06:11,965] [INFO] DFAST_QC completed!
[2023-03-19 02:06:11,965] [INFO] Total running time: 0h0m59s