[2023-03-16 06:12:34,970] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:12:34,974] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:12:34,974] [INFO] DQC Reference Directory: /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference
[2023-03-16 06:12:36,624] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:12:36,625] [INFO] Task started: Prodigal
[2023-03-16 06:12:36,625] [INFO] Running command: cat /var/lib/cwl/stg9b9b6411-23ab-4950-bcd9-f9dc9df98fc4/OceanDNA-b17180.fa | prodigal -d OceanDNA-b17180/cds.fna -a OceanDNA-b17180/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:12:39,276] [INFO] Task succeeded: Prodigal
[2023-03-16 06:12:39,276] [INFO] Task started: HMMsearch
[2023-03-16 06:12:39,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b17180/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/reference_markers.hmm OceanDNA-b17180/protein.faa > /dev/null
[2023-03-16 06:12:39,474] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:12:39,474] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9b9b6411-23ab-4950-bcd9-f9dc9df98fc4/OceanDNA-b17180.fa]
[2023-03-16 06:12:39,499] [INFO] Query marker FASTA was written to OceanDNA-b17180/markers.fasta
[2023-03-16 06:12:39,501] [INFO] Task started: Blastn
[2023-03-16 06:12:39,501] [INFO] Running command: blastn -query OceanDNA-b17180/markers.fasta -db /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/reference_markers.fasta -out OceanDNA-b17180/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:12:41,820] [INFO] Task succeeded: Blastn
[2023-03-16 06:12:41,836] [INFO] Selected 9 target genomes.
[2023-03-16 06:12:41,836] [INFO] Target genome list was writen to OceanDNA-b17180/target_genomes.txt
[2023-03-16 06:12:41,841] [INFO] Task started: fastANI
[2023-03-16 06:12:41,842] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b9b6411-23ab-4950-bcd9-f9dc9df98fc4/OceanDNA-b17180.fa --refList OceanDNA-b17180/target_genomes.txt --output OceanDNA-b17180/fastani_result.tsv --threads 1
[2023-03-16 06:12:44,554] [INFO] Task succeeded: fastANI
[2023-03-16 06:12:44,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:12:44,554] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:12:44,610] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2023-03-16 06:12:44,611] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-16 06:12:44,611] [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
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	97.914	62	69	95	conclusive
Jeotgalicoccus aerolatus	strain=CIP 111750	GCA_903994055.1	709510	709510	type	True	97.914	62	69	95	conclusive
Jeotgalicoccus aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	97.914	62	69	95	conclusive
Jeotgalicoccus halotolerans	strain=DSM 17274	GCA_003387165.1	157227	157227	type	True	83.5341	56	69	95	below_threshold
Jeotgalicoccus coquinae	strain=CCM 7682	GCA_014635225.1	709509	709509	type	True	81.8071	52	69	95	below_threshold
Jeotgalicoccus coquinae	strain=CIP 111751	GCA_903994065.1	709509	709509	type	True	81.7463	53	69	95	below_threshold
Jeotgalicoccus psychrophilus	strain=DSM 19085	GCA_000425845.1	157228	157228	type	True	81.179	59	69	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:12:44,612] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17180/tc_result.tsv
[2023-03-16 06:12:44,615] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:12:44,615] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:12:44,615] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/checkm_data
[2023-03-16 06:12:44,616] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:12:44,619] [INFO] Task started: CheckM
[2023-03-16 06:12:44,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17180/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17180/checkm_input OceanDNA-b17180/checkm_result
[2023-03-16 06:13:01,967] [INFO] Task succeeded: CheckM
[2023-03-16 06:13:01,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 46.42%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 06:13:02,009] [INFO] ===== Completeness check finished =====
[2023-03-16 06:13:02,009] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:13:02,009] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17180/markers.fasta)
[2023-03-16 06:13:02,009] [INFO] Task started: Blastn
[2023-03-16 06:13:02,009] [INFO] Running command: blastn -query OceanDNA-b17180/markers.fasta -db /var/lib/cwl/stgcce898d1-831c-4d72-8ae2-f395d4b802a8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17180/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:13:03,058] [INFO] Task succeeded: Blastn
[2023-03-16 06:13:03,062] [INFO] Selected 9 target genomes.
[2023-03-16 06:13:03,062] [INFO] Target genome list was writen to OceanDNA-b17180/target_genomes_gtdb.txt
[2023-03-16 06:13:03,073] [INFO] Task started: fastANI
[2023-03-16 06:13:03,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b9b6411-23ab-4950-bcd9-f9dc9df98fc4/OceanDNA-b17180.fa --refList OceanDNA-b17180/target_genomes_gtdb.txt --output OceanDNA-b17180/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:13:06,051] [INFO] Task succeeded: fastANI
[2023-03-16 06:13:06,056] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 06:13:06,056] [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_014635205.1	s__Jeotgalicoccus aerolatus	97.914	62	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	conclusive
GCF_003387165.1	s__Jeotgalicoccus halotolerans	83.5341	56	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	N/A	N/A	N/A	N/A	1	-
GCA_004570955.1	s__Jeotgalicoccus nanhaiensis	82.7012	56	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	96.2898	99.28	98.57	0.98	0.96	3	-
GCF_014207425.1	s__Jeotgalicoccus coquinae	81.9035	51	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	100.00	100.00	1.00	1.00	3	-
GCA_003513765.1	s__Jeotgalicoccus sp003513765	81.2526	55	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425845.1	s__Jeotgalicoccus psychrophilus	81.2493	58	69	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	97.52	97.52	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-03-16 06:13:06,058] [INFO] GTDB search result was written to OceanDNA-b17180/result_gtdb.tsv
[2023-03-16 06:13:06,063] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:13:06,067] [INFO] DFAST_QC result json was written to OceanDNA-b17180/dqc_result.json
[2023-03-16 06:13:06,067] [INFO] DFAST_QC completed!
[2023-03-16 06:13:06,067] [INFO] Total running time: 0h0m31s