[2023-03-15 06:50:51,567] [INFO] DFAST_QC pipeline started.
[2023-03-15 06:50:51,571] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 06:50:51,571] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference
[2023-03-15 06:50:53,472] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 06:50:53,473] [INFO] Task started: Prodigal
[2023-03-15 06:50:53,473] [INFO] Running command: cat /var/lib/cwl/stgc0ca0fd2-72e4-4b6a-960e-d6992af42462/OceanDNA-b23088.fa | prodigal -d OceanDNA-b23088/cds.fna -a OceanDNA-b23088/protein.faa -g 11 -q > /dev/null
[2023-03-15 06:51:26,400] [INFO] Task succeeded: Prodigal
[2023-03-15 06:51:26,401] [INFO] Task started: HMMsearch
[2023-03-15 06:51:26,401] [INFO] Running command: hmmsearch --tblout OceanDNA-b23088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/reference_markers.hmm OceanDNA-b23088/protein.faa > /dev/null
[2023-03-15 06:51:26,632] [INFO] Task succeeded: HMMsearch
[2023-03-15 06:51:26,632] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc0ca0fd2-72e4-4b6a-960e-d6992af42462/OceanDNA-b23088.fa]
[2023-03-15 06:51:26,691] [INFO] Query marker FASTA was written to OceanDNA-b23088/markers.fasta
[2023-03-15 06:51:26,692] [INFO] Task started: Blastn
[2023-03-15 06:51:26,692] [INFO] Running command: blastn -query OceanDNA-b23088/markers.fasta -db /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/reference_markers.fasta -out OceanDNA-b23088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:51:27,245] [INFO] Task succeeded: Blastn
[2023-03-15 06:51:27,259] [INFO] Selected 20 target genomes.
[2023-03-15 06:51:27,259] [INFO] Target genome list was writen to OceanDNA-b23088/target_genomes.txt
[2023-03-15 06:51:27,320] [INFO] Task started: fastANI
[2023-03-15 06:51:27,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ca0fd2-72e4-4b6a-960e-d6992af42462/OceanDNA-b23088.fa --refList OceanDNA-b23088/target_genomes.txt --output OceanDNA-b23088/fastani_result.tsv --threads 1
[2023-03-15 06:51:45,287] [INFO] Task succeeded: fastANI
[2023-03-15 06:51:45,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 06:51:45,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 06:51:45,291] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 06:51:45,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 06:51:45,291] [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
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	74.7857	71	1093	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 06:51:45,296] [INFO] DFAST Taxonomy check result was written to OceanDNA-b23088/tc_result.tsv
[2023-03-15 06:51:45,305] [INFO] ===== Taxonomy check completed =====
[2023-03-15 06:51:45,305] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 06:51:45,305] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/checkm_data
[2023-03-15 06:51:45,306] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 06:51:45,323] [INFO] Task started: CheckM
[2023-03-15 06:51:45,323] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b23088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b23088/checkm_input OceanDNA-b23088/checkm_result
[2023-03-15 06:53:04,704] [INFO] Task succeeded: CheckM
[2023-03-15 06:53:04,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.08%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 06:53:04,742] [INFO] ===== Completeness check finished =====
[2023-03-15 06:53:04,743] [INFO] ===== Start GTDB Search =====
[2023-03-15 06:53:04,743] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b23088/markers.fasta)
[2023-03-15 06:53:04,744] [INFO] Task started: Blastn
[2023-03-15 06:53:04,744] [INFO] Running command: blastn -query OceanDNA-b23088/markers.fasta -db /var/lib/cwl/stg9a55db6c-04a2-47a7-8b74-215318ffb2a2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b23088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 06:53:05,569] [INFO] Task succeeded: Blastn
[2023-03-15 06:53:05,574] [INFO] Selected 14 target genomes.
[2023-03-15 06:53:05,574] [INFO] Target genome list was writen to OceanDNA-b23088/target_genomes_gtdb.txt
[2023-03-15 06:53:05,820] [INFO] Task started: fastANI
[2023-03-15 06:53:05,820] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ca0fd2-72e4-4b6a-960e-d6992af42462/OceanDNA-b23088.fa --refList OceanDNA-b23088/target_genomes_gtdb.txt --output OceanDNA-b23088/fastani_result_gtdb.tsv --threads 1
[2023-03-15 06:53:16,050] [INFO] Task succeeded: fastANI
[2023-03-15 06:53:16,058] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 06:53:16,059] [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_016794425.1	s__JAEUHS01 sp016794425	76.6308	137	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794035.1	s__JAEUHS01 sp016794035	76.503	130	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003235605.1	s__SZUA-250 sp003235605	76.4693	69	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__SZUA-250	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713175.1	s__JADJPQ01 sp016713175	76.392	126	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJPQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235155.1	s__JACRLW01 sp016235155	76.3285	133	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JACRLW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051855.1	s__GCA-2684655 sp011051855	76.3142	92	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__GCA-2684655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716265.1	s__JADJWQ01 sp016716265	76.3007	166	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JADJWQ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872675.1	s__UBA2386 sp016872675	76.2715	114	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795295.1	s__VGXW01 sp016795295	76.1444	90	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903925435.1	s__SXPK01 sp903925435	76.1383	62	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__SXPK01	95.0	98.22	98.21	0.68	0.68	3	-
GCA_016873195.1	s__VGXW01 sp016873195	76.0749	109	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__VGXW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794565.1	s__JAEUHS01 sp016794565	76.0117	124	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__JAEUHS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793305.1	s__UBA2386 sp016793305	75.818	98	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__UBA2386	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005776365.1	s__SXPK01 sp005776365	75.4986	52	1093	d__Bacteria;p__Planctomycetota;c__UBA1135;o__UBA2386;f__UBA2386;g__SXPK01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 06:53:16,059] [INFO] GTDB search result was written to OceanDNA-b23088/result_gtdb.tsv
[2023-03-15 06:53:16,059] [INFO] ===== GTDB Search completed =====
[2023-03-15 06:53:16,060] [INFO] DFAST_QC result json was written to OceanDNA-b23088/dqc_result.json
[2023-03-15 06:53:16,060] [INFO] DFAST_QC completed!
[2023-03-15 06:53:16,060] [INFO] Total running time: 0h2m24s