[2023-03-19 00:55:12,875] [INFO] DFAST_QC pipeline started.
[2023-03-19 00:55:12,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 00:55:12,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference
[2023-03-19 00:55:13,970] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 00:55:13,971] [INFO] Task started: Prodigal
[2023-03-19 00:55:13,971] [INFO] Running command: cat /var/lib/cwl/stg88874181-ec33-4a61-9af6-cc5f198e8900/OceanDNA-b11837.fa | prodigal -d OceanDNA-b11837/cds.fna -a OceanDNA-b11837/protein.faa -g 11 -q > /dev/null
[2023-03-19 00:55:31,295] [INFO] Task succeeded: Prodigal
[2023-03-19 00:55:31,295] [INFO] Task started: HMMsearch
[2023-03-19 00:55:31,295] [INFO] Running command: hmmsearch --tblout OceanDNA-b11837/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/reference_markers.hmm OceanDNA-b11837/protein.faa > /dev/null
[2023-03-19 00:55:31,470] [INFO] Task succeeded: HMMsearch
[2023-03-19 00:55:31,470] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg88874181-ec33-4a61-9af6-cc5f198e8900/OceanDNA-b11837.fa]
[2023-03-19 00:55:31,488] [INFO] Query marker FASTA was written to OceanDNA-b11837/markers.fasta
[2023-03-19 00:55:31,489] [INFO] Task started: Blastn
[2023-03-19 00:55:31,489] [INFO] Running command: blastn -query OceanDNA-b11837/markers.fasta -db /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/reference_markers.fasta -out OceanDNA-b11837/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:55:32,018] [INFO] Task succeeded: Blastn
[2023-03-19 00:55:32,019] [INFO] Selected 25 target genomes.
[2023-03-19 00:55:32,019] [INFO] Target genome list was writen to OceanDNA-b11837/target_genomes.txt
[2023-03-19 00:55:32,031] [INFO] Task started: fastANI
[2023-03-19 00:55:32,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg88874181-ec33-4a61-9af6-cc5f198e8900/OceanDNA-b11837.fa --refList OceanDNA-b11837/target_genomes.txt --output OceanDNA-b11837/fastani_result.tsv --threads 1
[2023-03-19 00:55:47,874] [INFO] Task succeeded: fastANI
[2023-03-19 00:55:47,874] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 00:55:47,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 00:55:47,874] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 00:55:47,874] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 00:55:47,875] [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 00:55:47,876] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11837/tc_result.tsv
[2023-03-19 00:55:47,877] [INFO] ===== Taxonomy check completed =====
[2023-03-19 00:55:47,878] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 00:55:47,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/checkm_data
[2023-03-19 00:55:47,881] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 00:55:48,026] [INFO] Task started: CheckM
[2023-03-19 00:55:48,026] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11837/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11837/checkm_input OceanDNA-b11837/checkm_result
[2023-03-19 00:56:34,864] [INFO] Task succeeded: CheckM
[2023-03-19 00:56:34,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 00:56:34,901] [INFO] ===== Completeness check finished =====
[2023-03-19 00:56:34,901] [INFO] ===== Start GTDB Search =====
[2023-03-19 00:56:34,901] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11837/markers.fasta)
[2023-03-19 00:56:34,902] [INFO] Task started: Blastn
[2023-03-19 00:56:34,902] [INFO] Running command: blastn -query OceanDNA-b11837/markers.fasta -db /var/lib/cwl/stg248e81c2-b3ee-4437-bc5b-9cb9c5daa726/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11837/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 00:56:35,674] [INFO] Task succeeded: Blastn
[2023-03-19 00:56:35,701] [INFO] Selected 13 target genomes.
[2023-03-19 00:56:35,702] [INFO] Target genome list was writen to OceanDNA-b11837/target_genomes_gtdb.txt
[2023-03-19 00:56:35,717] [INFO] Task started: fastANI
[2023-03-19 00:56:35,717] [INFO] Running command: fastANI --query /var/lib/cwl/stg88874181-ec33-4a61-9af6-cc5f198e8900/OceanDNA-b11837.fa --refList OceanDNA-b11837/target_genomes_gtdb.txt --output OceanDNA-b11837/fastani_result_gtdb.tsv --threads 1
[2023-03-19 00:56:40,428] [INFO] Task succeeded: fastANI
[2023-03-19 00:56:40,433] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-19 00:56:40,433] [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_002863125.1	s__UA16 sp002863125	98.0755	497	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	conclusive
GCA_002448555.1	s__UA16 sp002448555	92.478	431	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	99.35	99.35	0.96	0.96	2	-
GCA_002690915.1	s__UA16 sp002690915	80.9997	377	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	96.97	96.97	0.71	0.71	2	-
GCA_002420235.1	s__UA16 sp002420235	79.3597	225	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.27	97.82	0.87	0.83	4	-
GCA_905479395.1	s__UA16 sp905479395	76.6294	58	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	98.40	98.40	0.84	0.84	2	-
GCA_002863145.1	s__UBA11663 sp002863145	76.4354	51	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_016777435.1	s__UA16 sp016777435	76.3655	54	516	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-19 00:56:40,441] [INFO] GTDB search result was written to OceanDNA-b11837/result_gtdb.tsv
[2023-03-19 00:56:40,456] [INFO] ===== GTDB Search completed =====
[2023-03-19 00:56:40,466] [INFO] DFAST_QC result json was written to OceanDNA-b11837/dqc_result.json
[2023-03-19 00:56:40,466] [INFO] DFAST_QC completed!
[2023-03-19 00:56:40,466] [INFO] Total running time: 0h1m28s