[2023-03-17 09:05:02,527] [INFO] DFAST_QC pipeline started.
[2023-03-17 09:05:02,527] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 09:05:02,527] [INFO] DQC Reference Directory: /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference
[2023-03-17 09:05:03,734] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 09:05:03,734] [INFO] Task started: Prodigal
[2023-03-17 09:05:03,734] [INFO] Running command: cat /var/lib/cwl/stg40efff01-7ba0-46bd-915e-677ade24d070/OceanDNA-b22183.fa | prodigal -d OceanDNA-b22183/cds.fna -a OceanDNA-b22183/protein.faa -g 11 -q > /dev/null
[2023-03-17 09:05:16,605] [INFO] Task succeeded: Prodigal
[2023-03-17 09:05:16,605] [INFO] Task started: HMMsearch
[2023-03-17 09:05:16,605] [INFO] Running command: hmmsearch --tblout OceanDNA-b22183/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/reference_markers.hmm OceanDNA-b22183/protein.faa > /dev/null
[2023-03-17 09:05:16,772] [INFO] Task succeeded: HMMsearch
[2023-03-17 09:05:16,772] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg40efff01-7ba0-46bd-915e-677ade24d070/OceanDNA-b22183.fa]
[2023-03-17 09:05:16,790] [INFO] Query marker FASTA was written to OceanDNA-b22183/markers.fasta
[2023-03-17 09:05:16,792] [INFO] Task started: Blastn
[2023-03-17 09:05:16,792] [INFO] Running command: blastn -query OceanDNA-b22183/markers.fasta -db /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/reference_markers.fasta -out OceanDNA-b22183/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:05:17,292] [INFO] Task succeeded: Blastn
[2023-03-17 09:05:17,293] [INFO] Selected 15 target genomes.
[2023-03-17 09:05:17,293] [INFO] Target genome list was writen to OceanDNA-b22183/target_genomes.txt
[2023-03-17 09:05:17,374] [INFO] Task started: fastANI
[2023-03-17 09:05:17,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg40efff01-7ba0-46bd-915e-677ade24d070/OceanDNA-b22183.fa --refList OceanDNA-b22183/target_genomes.txt --output OceanDNA-b22183/fastani_result.tsv --threads 1
[2023-03-17 09:05:25,690] [INFO] Task succeeded: fastANI
[2023-03-17 09:05:25,690] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 09:05:25,690] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 09:05:25,691] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 09:05:25,691] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 09:05:25,691] [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 09:05:25,691] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22183/tc_result.tsv
[2023-03-17 09:05:25,691] [INFO] ===== Taxonomy check completed =====
[2023-03-17 09:05:25,691] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 09:05:25,691] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/checkm_data
[2023-03-17 09:05:25,694] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 09:05:25,699] [INFO] Task started: CheckM
[2023-03-17 09:05:25,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22183/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22183/checkm_input OceanDNA-b22183/checkm_result
[2023-03-17 09:06:01,447] [INFO] Task succeeded: CheckM
[2023-03-17 09:06:01,447] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.57%
Contamintation: 0.90%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 09:06:01,449] [INFO] ===== Completeness check finished =====
[2023-03-17 09:06:01,450] [INFO] ===== Start GTDB Search =====
[2023-03-17 09:06:01,450] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22183/markers.fasta)
[2023-03-17 09:06:01,451] [INFO] Task started: Blastn
[2023-03-17 09:06:01,451] [INFO] Running command: blastn -query OceanDNA-b22183/markers.fasta -db /var/lib/cwl/stgba6f34f3-96c2-433a-9988-706c50735c8f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22183/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 09:06:02,132] [INFO] Task succeeded: Blastn
[2023-03-17 09:06:02,133] [INFO] Selected 13 target genomes.
[2023-03-17 09:06:02,133] [INFO] Target genome list was writen to OceanDNA-b22183/target_genomes_gtdb.txt
[2023-03-17 09:06:02,235] [INFO] Task started: fastANI
[2023-03-17 09:06:02,235] [INFO] Running command: fastANI --query /var/lib/cwl/stg40efff01-7ba0-46bd-915e-677ade24d070/OceanDNA-b22183.fa --refList OceanDNA-b22183/target_genomes_gtdb.txt --output OceanDNA-b22183/fastani_result_gtdb.tsv --threads 1
[2023-03-17 09:06:09,328] [INFO] Task succeeded: fastANI
[2023-03-17 09:06:09,333] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 09:06:09,333] [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_002709295.1	s__GCA-002862325 sp002709295	80.0612	431	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683195.1	s__GCA-002862325 sp002683195	78.0321	235	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685335.1	s__GCA-002862325 sp002685335	77.7883	132	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002690755.1	s__UBA12014 sp002690755	77.7173	200	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	99.96	99.96	0.92	0.92	2	-
GCA_002862325.1	s__GCA-002862325 sp002862325	77.4883	167	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-002862325	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002684755.1	s__UBA12014 sp002684755	77.4664	177	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__UBA12014	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002711415.1	s__GCA-2711415 sp002711415	75.9276	56	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__GCA-2711415	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124975.1	s__QWPT01 sp016124975	75.8772	75	670	d__Bacteria;p__Planctomycetota;c__Phycisphaerae;o__Phycisphaerales;f__SM1A02;g__QWPT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 09:06:09,333] [INFO] GTDB search result was written to OceanDNA-b22183/result_gtdb.tsv
[2023-03-17 09:06:09,333] [INFO] ===== GTDB Search completed =====
[2023-03-17 09:06:09,334] [INFO] DFAST_QC result json was written to OceanDNA-b22183/dqc_result.json
[2023-03-17 09:06:09,334] [INFO] DFAST_QC completed!
[2023-03-17 09:06:09,334] [INFO] Total running time: 0h1m7s