[2023-03-16 06:33:32,012] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:33:32,012] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:33:32,012] [INFO] DQC Reference Directory: /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference
[2023-03-16 06:33:33,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:33:33,193] [INFO] Task started: Prodigal
[2023-03-16 06:33:33,193] [INFO] Running command: cat /var/lib/cwl/stg5c0f510e-055a-4eae-a29f-0f81b2310060/OceanDNA-b45582.fa | prodigal -d OceanDNA-b45582/cds.fna -a OceanDNA-b45582/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:34:06,072] [INFO] Task succeeded: Prodigal
[2023-03-16 06:34:06,073] [INFO] Task started: HMMsearch
[2023-03-16 06:34:06,073] [INFO] Running command: hmmsearch --tblout OceanDNA-b45582/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/reference_markers.hmm OceanDNA-b45582/protein.faa > /dev/null
[2023-03-16 06:34:06,281] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:34:06,281] [INFO] Found 6/6 markers.
[2023-03-16 06:34:06,307] [INFO] Query marker FASTA was written to OceanDNA-b45582/markers.fasta
[2023-03-16 06:34:06,308] [INFO] Task started: Blastn
[2023-03-16 06:34:06,309] [INFO] Running command: blastn -query OceanDNA-b45582/markers.fasta -db /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/reference_markers.fasta -out OceanDNA-b45582/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:34:06,823] [INFO] Task succeeded: Blastn
[2023-03-16 06:34:06,824] [INFO] Selected 16 target genomes.
[2023-03-16 06:34:06,824] [INFO] Target genome list was writen to OceanDNA-b45582/target_genomes.txt
[2023-03-16 06:34:06,835] [INFO] Task started: fastANI
[2023-03-16 06:34:06,835] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0f510e-055a-4eae-a29f-0f81b2310060/OceanDNA-b45582.fa --refList OceanDNA-b45582/target_genomes.txt --output OceanDNA-b45582/fastani_result.tsv --threads 1
[2023-03-16 06:34:17,106] [INFO] Task succeeded: fastANI
[2023-03-16 06:34:17,106] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:34:17,106] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:34:17,106] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:34:17,106] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 06:34:17,106] [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
--------------------------------------------------------------------------------
[2023-03-16 06:34:17,107] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45582/tc_result.tsv
[2023-03-16 06:34:17,107] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:34:17,107] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:34:17,107] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/checkm_data
[2023-03-16 06:34:17,110] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:34:17,211] [INFO] Task started: CheckM
[2023-03-16 06:34:17,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45582/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45582/checkm_input OceanDNA-b45582/checkm_result
[2023-03-16 06:35:39,017] [INFO] Task succeeded: CheckM
[2023-03-16 06:35:39,018] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:35:39,020] [INFO] ===== Completeness check finished =====
[2023-03-16 06:35:39,021] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:35:39,021] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45582/markers.fasta)
[2023-03-16 06:35:39,022] [INFO] Task started: Blastn
[2023-03-16 06:35:39,022] [INFO] Running command: blastn -query OceanDNA-b45582/markers.fasta -db /var/lib/cwl/stg6386d656-7925-4cd3-b74d-962c7df6c797/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45582/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:35:39,711] [INFO] Task succeeded: Blastn
[2023-03-16 06:35:39,712] [INFO] Selected 26 target genomes.
[2023-03-16 06:35:39,713] [INFO] Target genome list was writen to OceanDNA-b45582/target_genomes_gtdb.txt
[2023-03-16 06:35:39,761] [INFO] Task started: fastANI
[2023-03-16 06:35:39,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c0f510e-055a-4eae-a29f-0f81b2310060/OceanDNA-b45582.fa --refList OceanDNA-b45582/target_genomes_gtdb.txt --output OceanDNA-b45582/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:35:52,240] [INFO] Task succeeded: fastANI
[2023-03-16 06:35:52,244] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:35:52,244] [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_018645725.1	s__MB11C04 sp018645725	83.9001	740	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722545.1	s__MB11C04 sp002722545	79.8524	414	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002500665.1	s__MB11C04 sp002500665	79.6286	363	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__MB11C04	95.0	98.37	95.55	0.93	0.84	7	-
GCA_002730975.1	s__GCA-2730975 sp002730975	78.495	110	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__GCA-2730975	95.0	99.68	99.68	0.85	0.85	2	-
GCA_002716045.1	s__UBA2993 sp002716045	76.4318	65	1180	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__MB11C04;g__UBA2993	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:35:52,245] [INFO] GTDB search result was written to OceanDNA-b45582/result_gtdb.tsv
[2023-03-16 06:35:52,245] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:35:52,245] [INFO] DFAST_QC result json was written to OceanDNA-b45582/dqc_result.json
[2023-03-16 06:35:52,246] [INFO] DFAST_QC completed!
[2023-03-16 06:35:52,246] [INFO] Total running time: 0h2m20s