[2023-03-18 07:54:30,547] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:54:30,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:54:30,548] [INFO] DQC Reference Directory: /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference
[2023-03-18 07:54:32,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:54:32,276] [INFO] Task started: Prodigal
[2023-03-18 07:54:32,277] [INFO] Running command: cat /var/lib/cwl/stg10d8cffc-45d2-4cdb-ad82-bc386e07808d/OceanDNA-b45095.fa | prodigal -d OceanDNA-b45095/cds.fna -a OceanDNA-b45095/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:54:39,592] [INFO] Task succeeded: Prodigal
[2023-03-18 07:54:39,593] [INFO] Task started: HMMsearch
[2023-03-18 07:54:39,593] [INFO] Running command: hmmsearch --tblout OceanDNA-b45095/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/reference_markers.hmm OceanDNA-b45095/protein.faa > /dev/null
[2023-03-18 07:54:39,760] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:54:39,761] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg10d8cffc-45d2-4cdb-ad82-bc386e07808d/OceanDNA-b45095.fa]
[2023-03-18 07:54:39,779] [INFO] Query marker FASTA was written to OceanDNA-b45095/markers.fasta
[2023-03-18 07:54:39,780] [INFO] Task started: Blastn
[2023-03-18 07:54:39,780] [INFO] Running command: blastn -query OceanDNA-b45095/markers.fasta -db /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/reference_markers.fasta -out OceanDNA-b45095/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:54:40,299] [INFO] Task succeeded: Blastn
[2023-03-18 07:54:40,300] [INFO] Selected 20 target genomes.
[2023-03-18 07:54:40,300] [INFO] Target genome list was writen to OceanDNA-b45095/target_genomes.txt
[2023-03-18 07:54:40,312] [INFO] Task started: fastANI
[2023-03-18 07:54:40,312] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d8cffc-45d2-4cdb-ad82-bc386e07808d/OceanDNA-b45095.fa --refList OceanDNA-b45095/target_genomes.txt --output OceanDNA-b45095/fastani_result.tsv --threads 1
[2023-03-18 07:54:52,539] [INFO] Task succeeded: fastANI
[2023-03-18 07:54:52,539] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:54:52,539] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:54:52,540] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:54:52,540] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 07:54:52,540] [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
--------------------------------------------------------------------------------
[2023-03-18 07:54:52,540] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45095/tc_result.tsv
[2023-03-18 07:54:52,540] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:54:52,540] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:54:52,540] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/checkm_data
[2023-03-18 07:54:52,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:54:52,593] [INFO] Task started: CheckM
[2023-03-18 07:54:52,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45095/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45095/checkm_input OceanDNA-b45095/checkm_result
[2023-03-18 07:55:17,705] [INFO] Task succeeded: CheckM
[2023-03-18 07:55:17,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.01%
Contamintation: 6.02%
Strain heterogeneity: 22.22%
--------------------------------------------------------------------------------
[2023-03-18 07:55:17,708] [INFO] ===== Completeness check finished =====
[2023-03-18 07:55:17,708] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:55:17,708] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45095/markers.fasta)
[2023-03-18 07:55:17,709] [INFO] Task started: Blastn
[2023-03-18 07:55:17,709] [INFO] Running command: blastn -query OceanDNA-b45095/markers.fasta -db /var/lib/cwl/stg121f4017-b2f3-47e8-9601-9854c2b31b13/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45095/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:55:18,422] [INFO] Task succeeded: Blastn
[2023-03-18 07:55:18,422] [INFO] Selected 9 target genomes.
[2023-03-18 07:55:18,422] [INFO] Target genome list was writen to OceanDNA-b45095/target_genomes_gtdb.txt
[2023-03-18 07:55:18,434] [INFO] Task started: fastANI
[2023-03-18 07:55:18,435] [INFO] Running command: fastANI --query /var/lib/cwl/stg10d8cffc-45d2-4cdb-ad82-bc386e07808d/OceanDNA-b45095.fa --refList OceanDNA-b45095/target_genomes_gtdb.txt --output OceanDNA-b45095/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:55:22,260] [INFO] Task succeeded: fastANI
[2023-03-18 07:55:22,264] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:55:22,264] [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_011522845.1	s__JCVI-SCAAA005 sp011522845	94.19	152	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002730365.1	s__JCVI-SCAAA005 sp002730365	93.4723	99	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450295.1	s__JCVI-SCAAA005 sp002450295	91.1782	136	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	96.73	95.52	0.71	0.67	8	-
GCA_002683655.1	s__JCVI-SCAAA005 sp002683655	89.9722	130	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	98.22	98.15	0.75	0.71	3	-
GCA_003541985.1	s__JCVI-SCAAA005 sp003541985	86.2812	122	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000224765.2	s__JCVI-SCAAA005 sp000224765	85.8116	125	167	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	97.34	96.08	0.74	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-18 07:55:22,264] [INFO] GTDB search result was written to OceanDNA-b45095/result_gtdb.tsv
[2023-03-18 07:55:22,265] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:55:22,265] [INFO] DFAST_QC result json was written to OceanDNA-b45095/dqc_result.json
[2023-03-18 07:55:22,265] [INFO] DFAST_QC completed!
[2023-03-18 07:55:22,265] [INFO] Total running time: 0h0m52s