[2023-03-15 05:51:32,068] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:51:32,068] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:51:32,068] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference
[2023-03-15 05:51:33,647] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:51:33,648] [INFO] Task started: Prodigal
[2023-03-15 05:51:33,648] [INFO] Running command: cat /var/lib/cwl/stgc5018af7-88da-4214-ae25-497e0f4c2fee/OceanDNA-b8708.fa | prodigal -d OceanDNA-b8708/cds.fna -a OceanDNA-b8708/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:51:40,183] [INFO] Task succeeded: Prodigal
[2023-03-15 05:51:40,184] [INFO] Task started: HMMsearch
[2023-03-15 05:51:40,184] [INFO] Running command: hmmsearch --tblout OceanDNA-b8708/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/reference_markers.hmm OceanDNA-b8708/protein.faa > /dev/null
[2023-03-15 05:51:40,360] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:51:40,360] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc5018af7-88da-4214-ae25-497e0f4c2fee/OceanDNA-b8708.fa]
[2023-03-15 05:51:40,373] [INFO] Query marker FASTA was written to OceanDNA-b8708/markers.fasta
[2023-03-15 05:51:40,374] [INFO] Task started: Blastn
[2023-03-15 05:51:40,374] [INFO] Running command: blastn -query OceanDNA-b8708/markers.fasta -db /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/reference_markers.fasta -out OceanDNA-b8708/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:51:41,957] [INFO] Task succeeded: Blastn
[2023-03-15 05:51:41,961] [INFO] Selected 25 target genomes.
[2023-03-15 05:51:41,961] [INFO] Target genome list was writen to OceanDNA-b8708/target_genomes.txt
[2023-03-15 05:51:41,977] [INFO] Task started: fastANI
[2023-03-15 05:51:41,977] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5018af7-88da-4214-ae25-497e0f4c2fee/OceanDNA-b8708.fa --refList OceanDNA-b8708/target_genomes.txt --output OceanDNA-b8708/fastani_result.tsv --threads 1
[2023-03-15 05:51:56,387] [INFO] Task succeeded: fastANI
[2023-03-15 05:51:56,388] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:51:56,388] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:51:56,388] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:51:56,388] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 05:51:56,388] [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
--------------------------------------------------------------------------------
[2023-03-15 05:51:56,389] [INFO] DFAST Taxonomy check result was written to OceanDNA-b8708/tc_result.tsv
[2023-03-15 05:51:56,390] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:51:56,390] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:51:56,390] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/checkm_data
[2023-03-15 05:51:56,394] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:51:56,397] [INFO] Task started: CheckM
[2023-03-15 05:51:56,397] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b8708/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b8708/checkm_input OceanDNA-b8708/checkm_result
[2023-03-15 05:52:18,592] [INFO] Task succeeded: CheckM
[2023-03-15 05:52:18,593] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 05:52:18,645] [INFO] ===== Completeness check finished =====
[2023-03-15 05:52:18,645] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:52:18,645] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b8708/markers.fasta)
[2023-03-15 05:52:18,647] [INFO] Task started: Blastn
[2023-03-15 05:52:18,647] [INFO] Running command: blastn -query OceanDNA-b8708/markers.fasta -db /var/lib/cwl/stgbd818621-51c7-40ba-b06f-305fe68d0c17/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b8708/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:52:19,396] [INFO] Task succeeded: Blastn
[2023-03-15 05:52:19,400] [INFO] Selected 10 target genomes.
[2023-03-15 05:52:19,400] [INFO] Target genome list was writen to OceanDNA-b8708/target_genomes_gtdb.txt
[2023-03-15 05:52:19,409] [INFO] Task started: fastANI
[2023-03-15 05:52:19,409] [INFO] Running command: fastANI --query /var/lib/cwl/stgc5018af7-88da-4214-ae25-497e0f4c2fee/OceanDNA-b8708.fa --refList OceanDNA-b8708/target_genomes_gtdb.txt --output OceanDNA-b8708/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:52:21,880] [INFO] Task succeeded: fastANI
[2023-03-15 05:52:21,886] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 05:52:21,886] [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_902560045.1	s__MED-G13 sp902560045	95.4681	239	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.04	98.52	0.67	0.66	3	conclusive
GCA_902557655.1	s__MED-G13 sp902557655	94.109	289	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	99.84	99.84	0.82	0.82	2	-
GCA_902510475.1	s__MED-G13 sp902510475	92.9841	247	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509675.1	s__MED-G13 sp902509675	81.7763	186	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697255.1	s__MED-G13 sp002697255	81.0155	239	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902510415.1	s__MED-G13 sp902510415	80.1624	153	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	98.10	98.10	0.69	0.69	2	-
GCA_902626365.1	s__MED-G13 sp902626365	79.1827	149	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	96.07	96.07	0.74	0.74	2	-
GCA_902519075.1	s__MED-G13 sp902519075	79.1821	154	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902604715.1	s__MED-G13 sp902604715	79.0116	158	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	97.66	97.66	0.81	0.81	2	-
GCA_902526075.1	s__MED-G13 sp902526075	78.3266	137	353	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MED-G13	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:52:21,887] [INFO] GTDB search result was written to OceanDNA-b8708/result_gtdb.tsv
[2023-03-15 05:52:21,888] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:52:21,891] [INFO] DFAST_QC result json was written to OceanDNA-b8708/dqc_result.json
[2023-03-15 05:52:21,891] [INFO] DFAST_QC completed!
[2023-03-15 05:52:21,891] [INFO] Total running time: 0h0m50s