[2023-03-15 10:52:57,317] [INFO] DFAST_QC pipeline started.
[2023-03-15 10:52:57,317] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 10:52:57,318] [INFO] DQC Reference Directory: /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference
[2023-03-15 10:52:58,869] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 10:52:58,870] [INFO] Task started: Prodigal
[2023-03-15 10:52:58,870] [INFO] Running command: cat /var/lib/cwl/stg1697d662-d076-4ce4-ac9c-da2e805fb8e0/OceanDNA-b37604.fa | prodigal -d OceanDNA-b37604/cds.fna -a OceanDNA-b37604/protein.faa -g 11 -q > /dev/null
[2023-03-15 10:53:17,013] [INFO] Task succeeded: Prodigal
[2023-03-15 10:53:17,013] [INFO] Task started: HMMsearch
[2023-03-15 10:53:17,014] [INFO] Running command: hmmsearch --tblout OceanDNA-b37604/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/reference_markers.hmm OceanDNA-b37604/protein.faa > /dev/null
[2023-03-15 10:53:17,220] [INFO] Task succeeded: HMMsearch
[2023-03-15 10:53:17,221] [INFO] Found 6/6 markers.
[2023-03-15 10:53:17,246] [INFO] Query marker FASTA was written to OceanDNA-b37604/markers.fasta
[2023-03-15 10:53:17,247] [INFO] Task started: Blastn
[2023-03-15 10:53:17,247] [INFO] Running command: blastn -query OceanDNA-b37604/markers.fasta -db /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/reference_markers.fasta -out OceanDNA-b37604/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:53:17,836] [INFO] Task succeeded: Blastn
[2023-03-15 10:53:17,837] [INFO] Selected 20 target genomes.
[2023-03-15 10:53:17,837] [INFO] Target genome list was writen to OceanDNA-b37604/target_genomes.txt
[2023-03-15 10:53:17,853] [INFO] Task started: fastANI
[2023-03-15 10:53:17,853] [INFO] Running command: fastANI --query /var/lib/cwl/stg1697d662-d076-4ce4-ac9c-da2e805fb8e0/OceanDNA-b37604.fa --refList OceanDNA-b37604/target_genomes.txt --output OceanDNA-b37604/fastani_result.tsv --threads 1
[2023-03-15 10:53:32,098] [INFO] Task succeeded: fastANI
[2023-03-15 10:53:32,098] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 10:53:32,099] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 10:53:32,112] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 10:53:32,112] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 10:53:32,113] [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
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	78.1651	226	951	95	below_threshold
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	77.9726	250	951	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	77.9335	246	951	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	77.6476	228	951	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	77.3578	214	951	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	76.9033	170	951	95	below_threshold
Halioglobus japonicus	strain=KCTC 23429	GCA_014652255.1	930805	930805	type	True	76.8896	171	951	95	below_threshold
Halioglobus japonicus	strain=S1-36	GCA_002869505.1	930805	930805	type	True	76.85	172	951	95	below_threshold
Pseudomonas thermotolerans	strain=DSM 14292	GCA_000364625.1	157784	157784	type	True	76.3631	85	951	95	below_threshold
Chromatocurvus halotolerans	strain=DSM 23344	GCA_004340525.1	1132028	1132028	type	True	76.1395	97	951	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	76.1344	86	951	95	below_threshold
Pseudomonas citronellolis	strain=LMG 18378	GCA_900112375.1	53408	53408	type	True	76.0404	125	951	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	76.0317	107	951	95	below_threshold
Pseudomonas citronellolis	strain=NBRC 103043	GCA_002091555.1	53408	53408	type	True	76.0298	126	951	95	below_threshold
Pseudomonas delhiensis	strain=RLD-1	GCA_900187975.1	366289	366289	type	True	75.9702	130	951	95	below_threshold
Pseudomonas delhiensis	strain=CCM 7361	GCA_900099945.1	366289	366289	type	True	75.9694	130	951	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	75.7679	62	951	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	75.754	77	951	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 10:53:32,113] [INFO] DFAST Taxonomy check result was written to OceanDNA-b37604/tc_result.tsv
[2023-03-15 10:53:32,113] [INFO] ===== Taxonomy check completed =====
[2023-03-15 10:53:32,113] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 10:53:32,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/checkm_data
[2023-03-15 10:53:32,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 10:53:32,182] [INFO] Task started: CheckM
[2023-03-15 10:53:32,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b37604/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b37604/checkm_input OceanDNA-b37604/checkm_result
[2023-03-15 10:54:18,893] [INFO] Task succeeded: CheckM
[2023-03-15 10:54:18,894] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.13%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 10:54:18,897] [INFO] ===== Completeness check finished =====
[2023-03-15 10:54:18,897] [INFO] ===== Start GTDB Search =====
[2023-03-15 10:54:18,897] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b37604/markers.fasta)
[2023-03-15 10:54:18,898] [INFO] Task started: Blastn
[2023-03-15 10:54:18,899] [INFO] Running command: blastn -query OceanDNA-b37604/markers.fasta -db /var/lib/cwl/stg84131f09-652c-46b5-ae5a-0b74f6c3ae9e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b37604/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 10:54:19,789] [INFO] Task succeeded: Blastn
[2023-03-15 10:54:19,790] [INFO] Selected 17 target genomes.
[2023-03-15 10:54:19,790] [INFO] Target genome list was writen to OceanDNA-b37604/target_genomes_gtdb.txt
[2023-03-15 10:54:19,809] [INFO] Task started: fastANI
[2023-03-15 10:54:19,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg1697d662-d076-4ce4-ac9c-da2e805fb8e0/OceanDNA-b37604.fa --refList OceanDNA-b37604/target_genomes_gtdb.txt --output OceanDNA-b37604/fastani_result_gtdb.tsv --threads 1
[2023-03-15 10:54:33,286] [INFO] Task succeeded: fastANI
[2023-03-15 10:54:33,297] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 10:54:33,297] [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_002699145.1	s__Halioglobus sp002699145	78.4513	385	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.96	99.96	0.98	0.98	2	-
GCF_004745945.1	s__Halioglobus sp004745945	78.2464	254	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064635.1	s__Parahaliea aestuarii	78.1814	225	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	78.1392	264	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003402235.1	s__Parahaliea mediterranea	77.9726	250	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	77.9468	245	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	77.6476	228	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	77.5811	236	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	77.3607	213	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983995.1	s__Halioglobus japonicus	76.9033	170	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	99.41	98.25	0.97	0.92	4	-
GCF_008370495.1	s__Halioglobus sp008370495	76.8093	200	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000364625.1	s__Pseudomonas_E thermotolerans	76.3631	85	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.25	99.24	0.93	0.93	3	-
GCF_902705825.1	s__Halioglobus japonicus_A	76.2413	107	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009763245.1	s__Pseudomonas_E sp009763245	76.1985	81	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112375.1	s__Pseudomonas citronellolis	76.0404	125	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	97.44	97.08	0.86	0.82	26	-
GCF_900187975.1	s__Pseudomonas delhiensis	75.9702	130	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas	95.078	98.79	97.59	0.94	0.89	3	-
GCF_900112645.1	s__Pseudomonas_E straminea	75.9625	61	951	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-15 10:54:33,297] [INFO] GTDB search result was written to OceanDNA-b37604/result_gtdb.tsv
[2023-03-15 10:54:33,297] [INFO] ===== GTDB Search completed =====
[2023-03-15 10:54:33,299] [INFO] DFAST_QC result json was written to OceanDNA-b37604/dqc_result.json
[2023-03-15 10:54:33,299] [INFO] DFAST_QC completed!
[2023-03-15 10:54:33,299] [INFO] Total running time: 0h1m36s